Jstacs - User contributions [en]

GeMoSeq-Examples

2025-11-19T14:52:49Z

Grau:

== GeMoSeq example run ==

We use a data set for yeast for an example run of GeMoSeq. As input of GeMoSeq, we need a reference genome and a library of reads mapped to that reference.
Here, we use the [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.fna.gz ''S. cerevisiae'' S288C reference genome R64] available from NCBI. For later evaluation of GeMoSeq prediction results, we also download the [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.gff.gz reference annotation].
As a sequencing library, we use the library with accession SRR8552464 available from the [https://www.ebi.ac.uk/ena/browser/home European Nucleotide archive] or [https://www.ncbi.nlm.nih.gov/sra NCBI Sequence Read Archive].

=== Mapping ===

''If you just want to test GeMoSeq, you can skip this step and proceed with the download provided at the end of this section.''

Before proceeding with GeMoSeq, these reads first need to be mapped to the reference genome. For yeast and other eukaryotes, we should use a splicing-aware mapping tool. Our current favourite is [https://github.com/alexdobin/STAR STAR] also available from [http://bioconda.github.io/recipes/star/README.html bioconda].

First, we need to index the reference genome with

STAR --runMode genomeGenerate --genomeDir yeast_index --genomeFastaFiles GCF_000146045.2_R64_genomic.fna --genomeSAindexNbases 10

Here, we specify <code>--genomeSAindexNbases 10</code> since the yeast genome is rather small.

Assuming reads have been stored in files <code>SRR8552464_1.fastq.gz</code> and <code>SRR8552464_2.fastq.gz</code>, we run STAR with the following command

STAR --genomeDir yeast_index --readFilesIn SRR8552464_1.fastq.gz SRR8552464_2.fastq.gz --readFilesCommand gunzip -c --outFileNamePrefix star/SRR8552464 --alignIntronMax 20000 --alignMatesGapMax 20000 --outSAMtype BAM SortedByCoordinate

Here, we limit the maximum intron size to 20000, since larger introns do not exist in yeast, but STAR tends to produce spurios long-split mappings, and let STAR output an already coordinate-sorted BAM file.

For convenience, we provide the resulting mapping file [http://www.jstacs.de/downloads/GeMoSeq/SRR8552464.bam for download].

=== Running GeMoSeq ===

The resulting mapping file and the reference genome used for mapping are input of GeMoSeq in the next step. For the next steps, we assume that the BAM file has been moved to a file <code>SRR8552464.bam</code> in the working directory (or has been downloaded from the provided link).

We leave most arguments at their defaults, calling GeMoSeq with

java -jar GeMoSeq-1.2.3.jar gemoseq g=GCF_000146045.2_R64_genomic.fna m=SRR8552464.bam s=FR_FIRST_STRAND threads=6 outdir=gemoseq

Here, we use the parameter <code>s=FR_FIRST_STRAND</code> to specify that this is a stranded library and set the number of threads to 6. The output directory is set to gemoseq.
At execution, GeMoSeq creates a temporary file with predictions in the working directory, which is later copied to the specified output directory together with a protocol of the GeMoSeq run. In the output directory, you will find the final predictions as a file <code>Transcript_Predictions.gff3</code>.

=== Evaluating prediction performance ===

To evaluate the accuracy of GeMoSeq predictions, we compare the GeMoSeq GFF against the yeast reference annotation. For this purpose, the GeMoSeq Jar file provides the [[GeMoMa]] Analyzer tool, which can be run with

java -jar GeMoSeq-1.2.3.jar Analyzer t=GCF_000146045.2_R64_genomic.gff p=gemoseq/Transcript_Predictions.gff3

The Analyzer tools outputs several metrics, including CDS sensitivity and precision, which are in this case 72.13 and 90.67, respectively.

== Using multiple libraries in combination with homology-based gene prediction ==

We use a [http://www.waterhouse-lab.com/Benth_download_2025/NbLab360.genome.fasta.gz recently published genome] of a ''Nicotiana benthamiana'' lab strain ([https://doi.org/10.1038/s41477-023-01489-8]) to illustrate how GeMoSeq can be used to re-annotate a genome based on multiple sequencing libraries and in combination with the homology-based gene prediction of [[GeMoMa]].

In the [https://doi.org/10.1101/2025.02.27.640589 GeMoSeq preprint], we sampled 319 sequencing libraries for ''N. benthamiana'' for this purpose, and we provide the corresponding [https://www.ebi.ac.uk/ena/browser/home ENA] accession table [http://www.jstacs.de/downloads/GeMoSeq/N_benthamiana_datasets.xlsx for download].

All of these libraries need to be downloaded, mapped to the genome sequence, and strandedness needs to be determined. For mapping, we follow the same procedure as described for the GeMoSeq example run above. To determine strandedness, we use [https://subread.sourceforge.net/featureCounts.html featureCounts] applied to the previous [http://www.waterhouse-lab.com/Benth_download_2025/NbLab360.v103.gff3.gz genome annotation] with flags for either strand orientation and choose the one with the larger number of assigned reads, or unstranded if both yield roughly equal numbers of assigned reads.
The strand orientation that has been determined by this procedure is listed in column "type" of the [http://www.jstacs.de/downloads/GeMoSeq/N_benthamiana_datasets.xlsx accession table].

=== Applying GeMoSeq to individual libraries ===

Assuming that the mapped reads are stored in directories named by the accession of the sequencing run, namely <code>mappings/<accession>/Aligned.sortedByCoord.out.bam</code>, e.g., <code>mappings/DRR377420/Aligned.sortedByCoord.out.bam</code>, we need to call GeMoSeq for each of these mapping files independently. This can be achieved by a (bash) for loop over all BAM files or in parallel on a compute cluster using a scheduling system like slurm.

An individual GeMoSeq run would look like

java -jar GeMoSeq-1.2.3.jar gemoseq g=NbLab360.genome.fasta m=mappings/<accession>/Aligned.sortedByCoord.out.bam s=<strandedness> threads=6 outdir=gemoseq/<accession>

where <code><accession></code> refers to the accession and <code><strandedness></code> refers to the strand orientation of the current library.

For instance, library DRR377420 has strand orientation <code>FR_FIRST_STRAND</code> (see above), and the corresponding GeMoSeq call would be

java -jar GeMoSeq-1.2.3.jar gemoseq g=NbLab360.genome.fasta m=mappings/DRR377420/Aligned.sortedByCoord.out.bam s=FR_FIRST_STRAND threads=6 outdir=gemoseq/DRR377420

where we, again, choose the name of the output directory based on the accession of the sequencing run. Within that directory, each GeMoSeq run will produce a file <code>Transcript_Predictions.gff3</code> with the predicted gene models.

After GeMoSeq has been run for all mapping files, the resulting prediction files are located in <code>gemoseq/<accession>/Transcript_Predictions.gff3</code>.

=== Joining individual predictions ===

To yield a joint GeMoSeq prediction across all libraries, we join the individual predictions using the [[GeMoMa-Docs#GeMoMa_Annotation_Filter| GeMoMa Annotation Filter]] (GAF) tool of [[GeMoMa]], which also comes packaged with the GeMoSeq JAR file.
For future merging with homology-based GeMoMa predictions, we run the GAF tool twice, once with looser and once with stricter filtering criteria.

For the looser filtering, we specify

java -jar GeMoSeq-1.2.3.jar GAF p=DRR377420 g=gemoseq/DRR377420/Transcript_Predictions.gff3 ... p=SRR29507616 g=gemoseq/SRR29507616/Transcript_Predictions.gff3 f="start=='M' and stop=='*' and sumWeight>7 and (isNaN(tie) or tie==1)" atf="sumWeight>23" mnotpg=20 tf=true outdir=gemoseq_loose

where <code>...</code> indicates that the arguments <code>p</code> and <code>g</code> need to be repeated for each of the individual predictions.
The filtering criteria (parameter <code>f</code>) specify that each tranferred transcript must have a proper start and stop codon, must appear in more than 7 (of 319) individual predictions and may either be a single-exon transcript (<code>isNaN(tie)</code>) or have perfect support for all splice sites (<code>tie==1</code>). The parameter <code>atf</code> defines that alternative transcripts are only transferred, if they occur in at least 24 of 319 libraries, parameter <code>mnotpg</code> specifies the maximum number of transcripts per gene, and <code>tf=true</code> indicates that additional features (i.e., exons + CDS) should be tranferred to the final prediction.
After the GAF run, the joint predictions are stored in <code>gemoseq_loose/filtered_predictions.gff</code>.

For the stricter filtering, we use adapted parameters

java -jar GeMoSeq-1.2.3.jar GAF p=DRR377420 g=gemoseq/DRR377420/Transcript_Predictions.gff3 ... p=SRR29507616 g=gemoseq/SRR29507616/Transcript_Predictions.gff3 f="start=='M' and stop=='*' and sumWeight>30 and (isNaN(tie) or tie==1)" atf="sumWeight>70" mnotpg=20 tf=true outdir=gemoseq_strict

and obtain joint predictions in <code>gemoseq_strict/filtered_predictions.gff</code>.

=== Homology-based gene prediction ===

For homology-based gene prediction, we use [[GeMoMa]] for the reference species ''A. thaliana'', ''N. tabacum'', ''S. lycopersicum'', and two previous ''N. benthamiana'' genome versions (1.0.1 and 2.6.1).
These predictions are also joined using the GAF tool.

For details about using GeMoMa for homology-based gene prediction, please refer to [[GeMoMa-Docs]].

Here, we assume that for the homology-based predictions, we also obtain a loosely and a strictly filtered prediction file as <code>gemoma_loose/filtered_predictions.gff</code> and <code>gemoma_strict/filtered_predictions.gff</code>, respectively.

=== Merging RNA-seq-based and homology-based predictions ===

We finally merge the four previously obtained prediction files (loose and strict for GeMoSeq and GeMoMa, respectively) using the GeMoSeq Merge tool. We call

java -jar GeMoSeq-1.2.3.jar merge g=gemoma_loose/filtered_predictions.gff GeMoSeq=gemoseq_loose/filtered_predictions.gff m=annotate GeMoMa-strict=gemoma_strict/filtered_predictions.gff GeMoSeq-strict=gemoseq_strict/filtered_predictions.gff l=false outdir=final

where parameter <code>m=annotate</code> specifies that merged predictions should be annotated with their confidence (high, medium) and <code>l=false</code> indicates that low-confidence predictions should be excluded from the output. After running the Merge tool, final predictions can be found in <code>final/Merged_Predictions.gff</code>.

2025-11-11T16:00:50Z

Grau: Grau moved page GeMoRNA to GeMoSeq

GeMoRNA reconstructs genes and transcript models from mapped RNA-seq reads (in coordinate-sorted BAM format) and reports these in GFF format.

It is intended as a companion for the homology-based gene prediction program [[GeMoMa]].

In a typical workflow, predictions of transcript models may be obtained from GeMoRNA for a collection of BAM files individually and subsequently merged using the [[GeMoMa]] Annotation Filter (GAF). Optionally, homology-based gene prediction may be performed using [[GeMoMa]] and the resulting GFF files may be merged using the [[#Merge|Merge]] tool of GeMoRNA.

== Command line tool ==

''GeMoRNA is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.''

GeMoRNA and auxiliary tools are packaged in one [http://www.jstacs.de/downloads/GeMoRNA-1.2.1.jar runnable JAR] that may be run from the command line with
java -jar GeMoRNA-1.2.1.jar

which lists the tools available and usage information

Available tools:

gemorna - GeMoRNA
predictCDS - Predict CDS from GFF
GAF - GeMoMa Annotation Filter
Analyzer - Analyzer
merge - Merge

Syntax: java -jar GeMoRNA-1.2.1.jar <toolname> [<parameter=value> ...]

Further info about the tools is given with
java -jar GeMoRNA-1.2.1.jar <toolname> info

For tests of individual tools:
java -jar GeMoRNA-1.2.1.jar <toolname> test [<verbose>]

Tool parameters are listed with
java -jar GeMoRNA-1.2.1.jar <toolname>

You get a list of the tool parameters by calling GeMoRNA-1.2.1.jar with the corresponding tool name, e.g.,

java -jar GeMoRNA-1.2.1.jar gemorna

The meaning of the individual tool parameters is described below.
For convenience, we also include the [[GeMoMa]] tools Analyzer and GAF.

== Source code ==

The source code of GeMoRNA is available from the [https://github.com/Jstacs/Jstacs/tree/master/projects/gemorna Jstacs GitHub repository].

== GeMoRNA ==

Prediction of transcript models using GeMoRNA.

''GeMoRNA'' may be called with

java -jar GeMoRNA-1.2.1.jar gemorna

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna,fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mapped reads (Mapped Reads in BAM format, coordinate sorted, type = bam)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>s</td>
<td>Stranded (Library strandedness, range={FR_UNSTRANDED, FR_FIRST_STRAND, FR_SECOND_STRAND}, default = FR_UNSTRANDED)</td>
<td style="width:100px;">STRING</td>
</tr>
<tr style="vertical-align:top">
<td>l</td>
<td>Longest intron length (Length of the longest intron reported, default = 100000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>sil</td>
<td>Shortest intron length (Length of the shortest intron considered, default = 10)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>lr</td>
<td>Long reads (Long-read mode, default = false)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
<tr style="vertical-align:top">
<td>mnor</td>
<td>Minimum number of reads (Minimum number of reads required for an edge in the read graph, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfor</td>
<td>Minimum fraction of reads (Minimum fraction of reads relative to adjacent exons that must support an intron in the enumeration, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mnoir</td>
<td>Minimum number of intron reads (Minimum number of reads required for an intron, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfoir</td>
<td>Minimum fraction of intron reads (Minimum fraction of reads relative to adjacent exons for an intron to be considered, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>Percent explained (Percent of abundance that must be explained by transcript models after quantification, default = 0.9)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpg</td>
<td>Minimum reads per gene (Minimum abundance required for a gene to be reported, default = 40.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpt</td>
<td>Minimum reads per transcript (Minimum abundance required for a transcript to be reported, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>pa</td>
<td>Percent abundance (Minimum relative abundance required for a transcript to be reported, default = 0.05)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>sf</td>
<td>Successive fraction (Factor of the drop in abundance between successive transcript models, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrl</td>
<td>Maximum region length (Maximum length of a region considered before it is split, default = 750000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mfgl</td>
<td>Maximum filled gap length (Maximum length of a gap filled by dummy reads, default = 50)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>q</td>
<td>Quality filter (Minimum mapping quality required for a read to be considered, default = 40)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mpl</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>gp</td>
<td>Gene prefix (Prefix to add to all gene names, default = G)</td>
<td style="width:100px;">STRING</td>
</tr>
<tr style="vertical-align:top">
<td>gnwc</td>
<td>Gene names with chromosome (If true, gene names will be constructed as <Gene prefix><chr>.<geneNumber>. Gene numbers will be assigned successively across all chromosomes., default = false)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
<tr style="vertical-align:top">
<td>threads</td>
<td>The number of threads used for the tool, defaults to 1. Currently, I/O of GeMoRNA runs on a single thread and runtime is limited by I/O performance. Hence, running GeMoRNA with a large number of threads is not recommended. On our infrastructure, a number of 6 threads has been the sweet spot.</td>
<td>INT</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.2.1.jar gemorna g=<Genome> m=<Mapped_reads>

== Predict CDS from GFF ==

Prediction of CDSs using the longest-ORF heuristic based on an existing GFF or GTF file.

''Predict CDS from GFF'' may be called with

java -jar GeMoRNA-1.2.1.jar predictCDS

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna.fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>predicted annotation ("GFF or GTF file containing the predicted annotation", type = gff,gff3,gff.gz,gff3.gz,gtf,gtf.gz)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.2.1.jar predictCDS g=<Genome> p=<predicted_annotation>

== Merge ==

Merging GeMoRNA and GeMoMa predictions.

''Merge'' may be called with

java -jar GeMoRNA-1.2.1.jar merge

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>GeMoMa (GeMoMa predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA</td>
<td>GeMoRNA (GeMoRNA predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mode (, range={intersect, union, intermediate, annotate}, default = intersect)</td>
<td style="width:100px;">STRING</td></tr>
<tr><td></td><td colspan=2><table border=0 cellpadding=0 align="center" width="100%">
<tr><td colspan=3>No parameters for selection "intersect"</td></tr>
<tr><td colspan=3>No parameters for selection "union"</td></tr>
<tr><td colspan=3>Parameters for selection "intermediate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr><td colspan=3>Parameters for selection "annotate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>l</td>
<td>Low-confidence (include low-confidence predictions, default = true)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
</table></td></tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.2.1.jar merge g=<GeMoMa> GeMoRNA=<GeMoRNA>

== Version history ==

* [http://www.jstacs.de/downloads/GeMoRNA-1.0.jar Version 1.0]: initial version of GeMoRNA
* [http://www.jstacs.de/downloads/GeMoRNA-1.1.jar Version 1.1] (2025/04/15): changes in the following tools
** merge: include flag if low-confidence predictions will be included in "annotate" mode
** gemorna: allow to provide custom prefix for gene names and to include the chromosome into the gene names
* [http://www.jstacs.de/downloads/GeMoRNA-1.2.jar Version 1.2] (2025/05/12): changes in the following tools
** gemorna: fixed a problem where (incomplete) CDS would be predicted in transcripts without any proper stop codon
* Version 1.2.1 (2025/05/28): improved handling of exceptions in multi-thread mode

AnnoTALE

2025-09-03T15:11:14Z

Grau: /* Class Builders */

[[File:AnnoTALE.png|130px|left]]
Transcription activator-like effectors (TALEs) are virulence factors of plant-pathogenic Xanthomonas spp. that function as gene activators inside plant host cells.

AnnoTALE is a suite of applications for identifying and analysing TALEs in Xanthomonas genomes, for clustering TALEs into classes by their RVD sequences, for assigning novel TALEs to existing classes, for proposing TALE names using a unified nomenclature, and for predicting targets of individual TALEs and TALE classes.

AnnoTALE is available as a JavaFX-based stand-alone application with graphical user interface for interactive analysis sessions.
In addition, we provide a command line application that may be integrated into other pipelines.
Both use identical code for the actual analysis, ensuring consistent results between both versions.

If you use AnnoTALE, please cite:

Jan Grau, Maik Reschke, Annett Erkes, Jana Streubel, Richard D. Morgan, Geoffrey G. Wilson, Ralf Koebnik and Jens Boch. [http://www.nature.com/articles/srep21077 AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from ''Xanthomonas'' genomic sequences]. Scientific Reports 6:21077, DOI: 10.1038/srep21077, 2016.

For evolution-related studies using the comparative features of AnnoTALE, please also cite:

Annett Erkes, Maik Reschke, Jens Boch, and Jan Grau. [https://doi.org/10.1093/gbe/evx108 Evolution of transcription activator-like effectors in Xanthomonas oryzae]. Genome Biology and Evolution, 9(6):1599–1615, 2017.

If you use PrediTALE for predicting TALE targets, please also cite:

Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, and Jan Grau. [https://doi.org/10.1371/journal.pcbi.1007206 PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting]. PLOS Computational Biology, 15(7):1–31, 2019.

'''Important:''' If you would like to use the unified nomenclature of AnnoTALE in one of your publications including new TALEs or sequenced genomes, please contact us (grau@informatik.uni-halle.de) to organize the inclusion of your TALEs into the official class definition of AnnoTALE and to create stable TALE names that are unique to your TALEs.

== AnnoTALE with GUI ==

[[File:AnnoTALEscreenshot.jpg]]

AnnoTALE is based on the implementation of JavaFX in Java >=8.

We provide AnnoTALE as a runnable JAR file for those with a current version of Java 8 (at least update 45) on their machine.

For user's convenience, we also provide pre-packaged versions of AnnoTALE, which also include Java in the required version, for Mac OS X and Windows. Each of these versions is available two version with different memory requirements (2GB and 6GB). As long as the main memory (RAM) of your machine is sufficient, we recommend to use the 6GB version of AnnoTALE.

=== Download ===

''AnnoTALE is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.''

* [http://www.jstacs.de/downloads/AnnoTALE-1.5.jar Runnable Jar] (requires installed Java >= 8, update 45), may be run under Linux, macOS and Windows
* macOS app: [http://www.jstacs.de/downloads/AnnoTALE-1.5.app-2GB.zip 2GB version], [http://www.jstacs.de/downloads/AnnoTALE-1.5.app-6GB.zip 6GB version], ZIP archive containing a macOS app including AnnoTALE and all required Java modules. For running this app, it might be required to explicitly give it running permissions in "System Preferences" -> "Security & Privacy" -> "General", which should list AnnoTALE after the first (possibly unsuccessful) starting attempt. Approve opening AnnoTALE by clicking on the button "Open Anyway" next to it.
* Windows installer of AnnoTALE including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.5-2GB.exe 2GB version, 64bit Java], [http://www.jstacs.de/downloads/AnnoTALE-1.5-6GB.exe 6GB version, 64bit Java]
* Windows version without installer: [http://www.jstacs.de/downloads/AnnoTALE-1.5-win.zip 6GB version, 64bit Java], ZIP archive containing AnnoTALE, all required Java modules, and a Windows batch file. For starting AnnoTALE, double-click AnnoTALE.bat.

=== Source code ===

The AnnoTALE source code is available from [https://github.com/Jstacs/Jstacs/tree/master/projects/xanthogenomes github].

=== User Guide ===

We provide an [http://www.jstacs.de/downloads/AnnoTALE-UserGuide-1.0.pdf AnnoTALE User Guide] in PDF format, including a detailed description of all AnnoTALE tools and installation instructions.

== AnnoTALE command line application ==

The AnnoTALE command line application is available as a [http://www.jstacs.de/downloads/AnnoTALEcli-1.5.jar runnable Jar]. For running the program and a quick help, type

java -jar AnnoTALEcli-1.5.jar

For larger analyes, it might be necessary to increase the memory allocated by the JavaVM using the <code>-Xms</code> and <code>-Xmx</code> parameters, for instance
java -Xms512M -Xmx6G -jar AnnoTALEcli-1.5.jar

There is no separate User Guide for the AnnoTALE command line application, but the [http://www.jstacs.de/downloads/AnnoTALE-UserGuide-1.0.pdf User Guide for the GUI version] describes all AnnoTALE tools, their parameters and outputs, and those of the CLI version are identical.

You obtain a list of all AnnoTALE tools by calling

java -jar AnnoTALEcli-1.5.jar

Output:

Available tools:

predict - TALE Prediction
analyze - TALE Analysis
build - TALE Class Builder
loadAndView - Load and View TALE Classes
assign - TALE Class Assignment
rename - Rename TALEs in File
targets - Predict and Intersect Targets
presence - TALE Class Presence
repdiff - TALE Repeat Differences
preditale - PrediTALE
dertale - DerTALE

Syntax: java -jar AnnoTALEcli-1.5.jar <toolname> [<parameter=value> ...]

Further info about the tools is given with
java -jar AnnoTALEcli-1.5.jar <toolname> info

Tool parameters are listed with
java -jar AnnoTALEcli-1.5.jar <toolname>

You get a list of input parameters by calling AnnoTALEcli-1.5.jar with the corresponding tool name, e.g.,

java -jar AnnoTALEcli-1.5.jar predict

Output:

At least one parameter has not been set (correctly):

Parameters of tool "TALE Prediction" (predict):
g - Genome (The input Xanthomonas genome in FastA or Genbank format) = null
s - Strain (The name of the strain, will be used for annotated TALEs, OPTIONAL) = null
outdir - The output directory, defaults to the current working directory (.) = .

You get a description of each tool by calling AnnoTALEcli-1.5.jar with the corresponding tool name and keyword "info", e.g.,

java -jar AnnoTALEcli-1.5.jar predict info

Output:
A detailed description of all tools is available in the AnnoTALE User Guide (http://www.jstacs.de/downloads/AnnoTALE-UserGuide-1.0.pdf).

*TALE Prediction* predicts transcription activator-like effector (TALE) genes in an input sequence, typically a 'Xanthomonas' genome.

'TALE Prediction' is based in HMMer nucleotide HMM models that describe N-terminus, repeat region, and C-terminus of TALEs.

The input 'Genome' may be provided in FastA or Genbank format.
Optionally, you may provide a strain name that will be used in the temporary TALE names and names of output files.

Regardless of the input format, 'TALE Prediction' generates output in Genbank format containing the annotations of TALE genes. If the original input has already been a Genbank file, TALE annotations are added to the existing ones.
In addition, 'TALE Prediction' generates annotations in GFF format, and also outputs the DNA and AS sequences of the predicted TALEs in FastA format.

'TALE Prediction' tries hard to make the CDS annotation a proper gene model, starting from a start codon and ending with a Stop. If either start or stop codon are located within the originally predicted region that is homologous to TALE genes, this original hit region is still reported as mRNA.
Putative pseudo genes, e.g., with premature stop codons, are marked accordingly.

The TALE DNA sequences output of 'TALE Prediction' may serve as input of the 'TALE Analysis', 'TALE Class Builder', and 'TALE Class Assignment' tools.

If you experience problems using 'TALE Prediction', please contact us.

=== Standard pipeline ===

Assuming that your current working directory contains the AnnoTALEcli Jar file, a genome of interest (of a hypothetical 'Xoo' strain PXO999 with accesion CP1234567) in a FastA file "genome.fa", all rice promoters in a FastA file "Rice-promoters.fa", and a directory "out" designated to hold all output files, a typical AnnoTALE pipeline could look like

java -jar AnnoTALEcli-1.5.jar predict g=genome.fa outdir=out

java -jar AnnoTALEcli-1.5.jar analyze t=out/TALE_DNA_sequences.fasta outdir=out

java -jar AnnoTALEcli-1.5.jar loadAndView outdir=out

java -jar AnnoTALEcli-1.5.jar assign c=out/Class_builder_download.xml t=out/TALE_DNA_parts.fasta s="Xoo PXO999" a="CP1234567" outdir=out

java -jar AnnoTALEcli-1.5.jar rename r=out/TALE_names_\(Xoo_PXO999\).tsv i=out/Genbank__TALE_predictions.gb outdir=out

java -jar AnnoTALEcli-1.5.jar targets i=Rice-promoters.fa p="TALEs in class builder" c=out/Augmented_class_builder_\(Xoo_PXO999\).xml outdir=out

Afterwards, you find all output files of all those tools in the directory "out". The output files and directories are named in analogy to the names in the AnnoTALE GUI version (see [http://www.jstacs.de/downloads/AnnoTALE-UserGuide-1.0.pdf User Guide for the GUI version])

==Version history==

===AnnoTALE===
'''Version 1.5'''
* new "sensitive" mode of TALE Prediction tool, which may annotate TALEs in a wider range of Xanthomonas strains at the expense of an increased runtime; turned off by default
* significantly improved speed of TALE Class Assignment tool
* citation information for individual AnnoTALE tools available under a dedicated button in the GUI version and from the "info" command issued for individual tools in the command line version
* bugfix for TALE Prediction in rather fragmented genome assemblies, where TALE predictions may extend to the ends of contigs/sequences
* [http://www.jstacs.de/downloads/AnnoTALE-1.5.jar Runnable Jar] (requires installed Java >= 8, update 45), may be run under Linux, macOS and Windows
* macOS app: [http://www.jstacs.de/downloads/AnnoTALE-1.5.app-2GB.zip 2GB version], [http://www.jstacs.de/downloads/AnnoTALE-1.5.app-6GB.zip 6GB version], ZIP archive containing a macOS app including AnnoTALE and all required Java modules. For running this app, it might be required to explicitly give it running permissions in "System Preferences" -> "Security & Privacy" -> "General", which should list AnnoTALE after the first (possibly unsuccessful) starting attempt.
* Windows installer of AnnoTALE including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.5-2GB.exe 2GB version, 64bit Java], [http://www.jstacs.de/downloads/AnnoTALE-1.5-6GB.exe 6GB version, 64bit Java]
* Windows version without installer: [http://www.jstacs.de/downloads/AnnoTALE-1.5-win.zip 6GB version, 64bit Java], ZIP archive containing AnnoTALE, all required Java modules, and a Windows batch file. For starting AnnoTALE, double-click AnnoTALE.bat.

'''Version 1.4.1'''
* first version to use the updated Class Builder including a large number of recently sequence strains
* minor changes to the output of the 'Load and View TALE Classes' tool, now including the accessions in the TALE sequence output
* changes to the Class Builder format to account for the increased size of class hierarchy, which previously resulted in unnecessarily large files
* 32bit/1GB Windows version no longer included
* [http://www.jstacs.de/downloads/AnnoTALE-1.4.1.jar Runnable Jar] (requires Java 8, update 45 or greater)
* Mac-DMG of AnnoTALE including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.4.1-2GB.dmg 2GB version], [http://www.jstacs.de/downloads/AnnoTALE-1.4.1-6GB.dmg 6GB version]
* Windows installer of AnnoTALE including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.4.1-2GB.exe 2GB version, 64bit Java], [http://www.jstacs.de/downloads/AnnoTALE-1.4.1-6GB.exe 6GB version, 64bit Java]
* [http://www.jstacs.de/downloads/AnnoTALEcli-1.4.1.jar AnnoTALE 1.4.1 command line application]

'''Version 1.4:'''
* first version containing [[PrediTALE]] and DerTALE tools for target site prediction
* [http://www.jstacs.de/downloads/AnnoTALE-1.4.jar Runnable Jar] (requires Java 8, update 45 or greater)
* Mac-DMG of AnnoTALE including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.4-2GB.dmg 2GB version], [http://www.jstacs.de/downloads/AnnoTALE-1.4-6GB.dmg 6GB version]
* Windows installer of AnnoTALE including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.4-2GB.exe 2GB version, 64bit Java], [http://www.jstacs.de/downloads/AnnoTALE-1.4-6GB.exe 6GB version, 64bit Java]; in addition, we provide a [http://www.jstacs.de/downloads/AnnoTALE-1.4-1GB.exe 1GB version with 32bit Java] for earlier and 32bit versions of Windows. Please use this version only if absolutely necessary, as some tools may not work due to memory restrictions.
* [http://www.jstacs.de/downloads/AnnoTALEcli-1.4.jar AnnoTALE 1.4 command line application]

'''Version 1.3:'''
* [http://www.jstacs.de/downloads/AnnoTALE-1.3.jar AnnoTALE 1.3 Runnable Jar] (requires Java 8, update 45 or greater)
* Mac-DMG of AnnoTALE 1.3 including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.3-2GB.dmg AnnoTALE 1.3 2GB version], [http://www.jstacs.de/downloads/AnnoTALE-1.3-6GB.dmg AnnoTALE 1.3 6GB version]
* Windows installer of AnnoTALE 1.3 including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.3-2GB.exe AnnoTALE 1.3 2GB version, 64bit Java], [http://www.jstacs.de/downloads/AnnoTALE-1.3-6GB.exe AnnoTALE 1.3 6GB version, 64bit Java]; [http://www.jstacs.de/downloads/AnnoTALE-1.3-1GB.exe AnnoTALE 1.3 1GB version with 32bit Java]
* [http://www.jstacs.de/downloads/AnnoTALEcli-1.3.jar AnnoTALE 1.3 command line application]

Changes:
* modified format of Class Builder files allowing for faster download using the "Load and View TALE Classes" tool; old Class Builder files can still be loaded
* "TALE Class Presence" now also outputs a phylogenetic tree of strains based on TALEome similarities

'''Version 1.2:'''
* [http://www.jstacs.de/downloads/AnnoTALE-1.2.jar AnnoTALE 1.2 Runnable Jar] (requires Java 8, update 45 or greater)
* Mac-DMG of AnnoTALE 1.2 including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.2-2GB.dmg AnnoTALE 1.2 2GB version], [http://www.jstacs.de/downloads/AnnoTALE-1.2-6GB.dmg AnnoTALE 1.2 6GB version]
* Windows installer of AnnoTALE 1.2 including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.2-2GB.exe AnnoTALE 1.2 2GB version, 64bit Java], [http://www.jstacs.de/downloads/AnnoTALE-1.2-6GB.exe AnnoTALE 1.2 6GB version, 64bit Java]; [http://www.jstacs.de/downloads/AnnoTALE-1.2-1GB.exe AnnoTALE 1.2 1GB version with 32bit Java]
* [http://www.jstacs.de/downloads/AnnoTALEcli-1.2.jar AnnoTALE 1.2 command line application]

Changes:
* Results and loaded files may now be renamed in the GUI by clicking on the corresponding name in the "Data" panel
* Minor bugfixes and improvements of the GUI (Protocol may be erased, columns in "Data" panel renamed for clarity, consistency of paths in the open/save dialogs under Linux)
* Two new tools: "TALE Class Presence" and "TALE Repeat differences"

'''Version 1.1:'''

* [http://www.jstacs.de/downloads/AnnoTALE-1.1.jar AnnoTALE 1.1 Runnable Jar] (requires Java 8, update 45 or greater)
* Mac-DMG of AnnoTALE 1.1 including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.1-2GB.dmg AnnoTALE 1.1 2GB version], [http://www.jstacs.de/downloads/AnnoTALE-1.1-6GB.dmg AnnoTALE 1.1 6GB version]
* Windows installer of AnnoTALE 1.1 including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.1-2GB.exe AnnoTALE 1.1 2GB version, 64bit Java], [http://www.jstacs.de/downloads/AnnoTALE-1.1-6GB.exe AnnoTALE 1.1 6GB version, 64bit Java]; [http://www.jstacs.de/downloads/AnnoTALE-1.1-1GB.exe AnnoTALE 1.1 1GB version with 32bit Java]
* [http://www.jstacs.de/downloads/AnnoTALEcli-1.1.jar AnnoTALE 1.1 command line application]

Changes:
* Additional output for the "Load and View TALE Classes" tool
* "TALE Class Builder" and "TALE Class Assignment" now also accept RVD sequences (separated by dashes) as input. However, this is not recommended and some features (e.g., highlighting of aberrant repeats) will not be available. Only complete TALE DNA sequences will be accepted for inclusion into the official Class Builder.
* The internal help pages now link to the PDF User Guide

'''Version 1.0:'''

''Initial AnnoTALE release''

* [http://www.jstacs.de/downloads/AnnoTALE-1.0.jar AnnoTALE 1.0 Runnable Jar] (requires Java 8, update 45 or greater)
* Mac-DMG of AnnoTALE including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.0-2GB.dmg AnnoTALE 1.0 2GB version], [http://www.jstacs.de/downloads/AnnoTALE-1.0-6GB.dmg AnnoTALE 1.0 6GB version]
* Windows installer of AnnoTALE including Java: [http://www.jstacs.de/downloads/AnnoTALE-1.0-2GB.exe AnnoTALE 1.0 2GB version, 64bit Java], [http://www.jstacs.de/downloads/AnnoTALE-1.0-6GB.exe AnnoTALE 1.0 6GB version, 64bit Java]; [http://www.jstacs.de/downloads/AnnoTALE-1.0-1GB.exe AnnoTALE 1.0 1GB version with 32bit Java]
* [http://www.jstacs.de/downloads/AnnoTALEcli-1.0.jar AnnoTALE 1.0 command line application]

=== Class Builders ===

* [http://www.jstacs.de/downloads/class_definitions_01_09_2025.xml.gz Version 01/09/2025]: used for "Download current definition" in "Load and View TALE Classes" within AnnoTALE version 1.4.1 and later
* [http://www.jstacs.de/downloads/class_definitions_30_01_2024.xml.gz Version 30/01/2024]: compatible with AnnoTALE version 1.4.1 and later
* [http://www.jstacs.de/downloads/class_definitions_29_07_2022.xml.gz Version 29/07/2022]: compatible with AnnoTALE version 1.4.1 and later
* [http://www.jstacs.de/downloads/class_definitions_17_08_2021.xml.gz Version 17/08/2021]: compatible with AnnoTALE version 1.4.1 and later
* [http://www.jstacs.de/downloads/class_definitions_09_05_2021.xml.gz Version 09/05/2021]: compatible with AnnoTALE version 1.4.1 and later
* [http://www.jstacs.de/downloads/class_definitions_10_10_2020.xml.gz Version 10/10/2020]: compatible with AnnoTALE version 1.4.1 and later
* [http://www.jstacs.de/downloads/class_definitions_20_06_2019.xml.gz Version 20/06/2019]: compatible with AnnoTALE version 1.4.1 and later
* [http://www.jstacs.de/downloads/class_definitions_29_09_2018.xml.gz Version 29/09/2018]: used for "Download current definition" in "Load and View TALE Classes" within AnnoTALE version 1.3 and later
* [http://www.jstacs.de/downloads/class_definitions_09_03_2017.xml Version 09/03/2017]: used for "Download current definition" in "Load and View TALE Classes" within AnnoTALE version 1.2 and earlier
* [http://www.jstacs.de/downloads/class_definitions_11_03_2016.xml Version 03/11/2016]
* [http://www.jstacs.de/downloads/class_definitions_29_01_2016.xml Version 01/29/2016]
* [http://www.jstacs.de/downloads/class_definitions_19_10.xml Version 10/19/2015]: used in the AnnoTALE publication (Grau ''et al.'', Sci Rep, 2016)

2024-11-08T16:27:41Z

Grau:

GeMoSeq

2024-11-08T16:27:21Z

Grau:

== Command line tool ==

''GeMoRNA is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.''

GeMoRNA and auxiliary tools are packaged in one [http://www.jstacs.de/downloads/GeMoRNA-1.0.jar runnable JAR] that may be run from the command line with
java -jar GeMoRNA-1.0.jar

which lists the tools available and usage information

Available tools:

gemorna - GeMoRNA
predictCDS - Predict CDS from GFF
GAF - GeMoMa Annotation Filter
Analyzer - Analyzer
merge - Merge

Syntax: java -jar GeMoRNA-1.0.jar <toolname> [<parameter=value> ...]

Further info about the tools is given with
java -jar GeMoRNA-1.0.jar <toolname> info

For tests of individual tools:
java -jar GeMoRNA-1.0.jar <toolname> test [<verbose>]

Tool parameters are listed with
java -jar GeMoRNA-1.0.jar <toolname>

You get a list of the tool parameters by calling GeMoRNA-1.0.jar with the corresponding tool name, e.g.,

java -jar GeMoRNA-1.0.jar gemorna

The meaning of the individual tool parameters is described below.
For convenience, we also include the [GeMoMa] tools Analyzer and GAF.

== Source code ==

The source code of GeMoRNA is available from the [https://github.com/Jstacs/Jstacs/tree/master/projects/gemorna Jstacs GitHub repository].

== GeMoRNA ==

Prediction of transcript models using GeMoRNA.

''GeMoRNA'' may be called with

java -jar GeMoRNA-1.0.jar gemorna

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna,fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mapped reads (Mapped Reads in BAM format, coordinate sorted, type = bam)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>s</td>
<td>Stranded (Library strandedness, range={FR_UNSTRANDED, FR_FIRST_STRAND, FR_SECOND_STRAND}, default = FR_UNSTRANDED)</td>
<td style="width:100px;">STRING</td>
</tr>
<tr style="vertical-align:top">
<td>l</td>
<td>Longest intron length (Length of the longest intron reported, default = 100000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>sil</td>
<td>Shortest intron length (Length of the shortest intron considered, default = 10)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>lr</td>
<td>Long reads (Long-read mode, default = false)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
<tr style="vertical-align:top">
<td>mnor</td>
<td>Minimum number of reads (Minimum number of reads required for an edge in the read graph, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfor</td>
<td>Minimum fraction of reads (Minimum fraction of reads relative to adjacent exons that must support an intron in the enumeration, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mnoir</td>
<td>Minimum number of intron reads (Minimum number of reads required for an intron, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfoir</td>
<td>Minimum fraction of intron reads (Minimum fraction of reads relative to adjacent exons for an intron to be considered, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>Percent explained (Percent of abundance that must be explained by transcript models after quantification, default = 0.9)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpg</td>
<td>Minimum reads per gene (Minimum abundance required for a gene to be reported, default = 40.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpt</td>
<td>Minimum reads per transcript (Minimum abundance required for a transcript to be reported, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>pa</td>
<td>Percent abundance (Minimum relative abundance required for a transcript to be reported, default = 0.05)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>sf</td>
<td>Successive fraction (Factor of the drop in abundance between successive transcript models, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrl</td>
<td>Maximum region length (Maximum length of a region considered before it is split, default = 750000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mfgl</td>
<td>Maximum filled gap length (Maximum length of a gap filled by dummy reads, default = 50)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>q</td>
<td>Quality filter (Minimum mapping quality required for a read to be considered, default = 40)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mpl</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
<tr style="vertical-align:top">
<td>threads</td>
<td>The number of threads used for the tool, defaults to 1</td>
<td>INT</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar gemorna g=<Genome> m=<Mapped_reads>

== Predict CDS from GFF ==

Prediction of CDSs using the longest-ORF heuristic based on an existing GFF or GTF file.

''Predict CDS from GFF'' may be called with

java -jar GeMoRNA-1.0.jar predictCDS

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna.fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>predicted annotation ("GFF or GTF file containing the predicted annotation", type = gff,gff3,gff.gz,gff3.gz,gtf,gtf.gz)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar predictCDS g=<Genome> p=<predicted_annotation>

== Merge ==

Merging GeMoRNA and GeMoMa predictions.

''Merge'' may be called with

java -jar GeMoRNA-1.0.jar merge

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>GeMoMa (GeMoMa predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA</td>
<td>GeMoRNA (GeMoRNA predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mode (, range={intersect, union, intermediate, annotate}, default = intersect)</td>
<td style="width:100px;">STRING</td></tr>
<tr><td></td><td colspan=2><table border=0 cellpadding=0 align="center" width="100%">
<tr><td colspan=3>No parameters for selection "intersect"</td></tr>
<tr><td colspan=3>No parameters for selection "union"</td></tr>
<tr><td colspan=3>Parameters for selection "intermediate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr><td colspan=3>Parameters for selection "annotate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
</table></td></tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar merge g=<GeMoMa> GeMoRNA=<GeMoRNA>

GeMoSeq

2024-11-08T16:23:36Z

Grau:

== Command line tool ==

== Source code ==

The source code of GeMoRNA is available from the [https://github.com/Jstacs/Jstacs/tree/master/projects/gemorna Jstacs GitHub repository].

== GeMoRNA ==

Prediction of transcript models using GeMoRNA.

''GeMoRNA'' may be called with

java -jar GeMoRNA-1.0.jar gemorna

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna,fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mapped reads (Mapped Reads in BAM format, coordinate sorted, type = bam)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>s</td>
<td>Stranded (Library strandedness, range={FR_UNSTRANDED, FR_FIRST_STRAND, FR_SECOND_STRAND}, default = FR_UNSTRANDED)</td>
<td style="width:100px;">STRING</td>
</tr>
<tr style="vertical-align:top">
<td>l</td>
<td>Longest intron length (Length of the longest intron reported, default = 100000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>sil</td>
<td>Shortest intron length (Length of the shortest intron considered, default = 10)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>lr</td>
<td>Long reads (Long-read mode, default = false)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
<tr style="vertical-align:top">
<td>mnor</td>
<td>Minimum number of reads (Minimum number of reads required for an edge in the read graph, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfor</td>
<td>Minimum fraction of reads (Minimum fraction of reads relative to adjacent exons that must support an intron in the enumeration, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mnoir</td>
<td>Minimum number of intron reads (Minimum number of reads required for an intron, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfoir</td>
<td>Minimum fraction of intron reads (Minimum fraction of reads relative to adjacent exons for an intron to be considered, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>Percent explained (Percent of abundance that must be explained by transcript models after quantification, default = 0.9)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpg</td>
<td>Minimum reads per gene (Minimum abundance required for a gene to be reported, default = 40.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpt</td>
<td>Minimum reads per transcript (Minimum abundance required for a transcript to be reported, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>pa</td>
<td>Percent abundance (Minimum relative abundance required for a transcript to be reported, default = 0.05)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>sf</td>
<td>Successive fraction (Factor of the drop in abundance between successive transcript models, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrl</td>
<td>Maximum region length (Maximum length of a region considered before it is split, default = 750000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mfgl</td>
<td>Maximum filled gap length (Maximum length of a gap filled by dummy reads, default = 50)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>q</td>
<td>Quality filter (Minimum mapping quality required for a read to be considered, default = 40)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mpl</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
<tr style="vertical-align:top">
<td>threads</td>
<td>The number of threads used for the tool, defaults to 1</td>
<td>INT</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar gemorna g=<Genome> m=<Mapped_reads>

== Predict CDS from GFF ==

Prediction of CDSs using the longest-ORF heuristic based on an existing GFF or GTF file.

''Predict CDS from GFF'' may be called with

java -jar GeMoRNA-1.0.jar predictCDS

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna.fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>predicted annotation ("GFF or GTF file containing the predicted annotation", type = gff,gff3,gff.gz,gff3.gz,gtf,gtf.gz)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar predictCDS g=<Genome> p=<predicted_annotation>

== Merge ==

Merging GeMoRNA and GeMoMa predictions.

''Merge'' may be called with

java -jar GeMoRNA-1.0.jar merge

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>GeMoMa (GeMoMa predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA</td>
<td>GeMoRNA (GeMoRNA predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mode (, range={intersect, union, intermediate, annotate}, default = intersect)</td>
<td style="width:100px;">STRING</td></tr>
<tr><td></td><td colspan=2><table border=0 cellpadding=0 align="center" width="100%">
<tr><td colspan=3>No parameters for selection "intersect"</td></tr>
<tr><td colspan=3>No parameters for selection "union"</td></tr>
<tr><td colspan=3>Parameters for selection "intermediate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr><td colspan=3>Parameters for selection "annotate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
</table></td></tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar merge g=<GeMoMa> GeMoRNA=<GeMoRNA>

GeMoSeq

2024-11-08T16:21:51Z

Grau:

== GeMoRNA ==

Prediction of transcript models using GeMoRNA.

''GeMoRNA'' may be called with

java -jar GeMoRNA-1.0.jar gemorna

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna,fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mapped reads (Mapped Reads in BAM format, coordinate sorted, type = bam)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>s</td>
<td>Stranded (Library strandedness, range={FR_UNSTRANDED, FR_FIRST_STRAND, FR_SECOND_STRAND}, default = FR_UNSTRANDED)</td>
<td style="width:100px;">STRING</td>
</tr>
<tr style="vertical-align:top">
<td>l</td>
<td>Longest intron length (Length of the longest intron reported, default = 100000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>sil</td>
<td>Shortest intron length (Length of the shortest intron considered, default = 10)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>lr</td>
<td>Long reads (Long-read mode, default = false)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
<tr style="vertical-align:top">
<td>mnor</td>
<td>Minimum number of reads (Minimum number of reads required for an edge in the read graph, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfor</td>
<td>Minimum fraction of reads (Minimum fraction of reads relative to adjacent exons that must support an intron in the enumeration, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mnoir</td>
<td>Minimum number of intron reads (Minimum number of reads required for an intron, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfoir</td>
<td>Minimum fraction of intron reads (Minimum fraction of reads relative to adjacent exons for an intron to be considered, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>Percent explained (Percent of abundance that must be explained by transcript models after quantification, default = 0.9)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpg</td>
<td>Minimum reads per gene (Minimum abundance required for a gene to be reported, default = 40.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpt</td>
<td>Minimum reads per transcript (Minimum abundance required for a transcript to be reported, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>pa</td>
<td>Percent abundance (Minimum relative abundance required for a transcript to be reported, default = 0.05)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>sf</td>
<td>Successive fraction (Factor of the drop in abundance between successive transcript models, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrl</td>
<td>Maximum region length (Maximum length of a region considered before it is split, default = 750000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mfgl</td>
<td>Maximum filled gap length (Maximum length of a gap filled by dummy reads, default = 50)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>q</td>
<td>Quality filter (Minimum mapping quality required for a read to be considered, default = 40)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mpl</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
<tr style="vertical-align:top">
<td>threads</td>
<td>The number of threads used for the tool, defaults to 1</td>
<td>INT</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar gemorna g=<Genome> m=<Mapped_reads>

== Predict CDS from GFF ==

Prediction of CDSs using the longest-ORF heuristic based on an existing GFF or GTF file.

''Predict CDS from GFF'' may be called with

java -jar GeMoRNA-1.0.jar predictCDS

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna.fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>predicted annotation ("GFF or GTF file containing the predicted annotation", type = gff,gff3,gff.gz,gff3.gz,gtf,gtf.gz)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar predictCDS g=<Genome> p=<predicted_annotation>

== Merge ==

Merging GeMoRNA and GeMoMa predictions.

''Merge'' may be called with

java -jar GeMoRNA-1.0.jar merge

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>GeMoMa (GeMoMa predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA</td>
<td>GeMoRNA (GeMoRNA predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mode (, range={intersect, union, intermediate, annotate}, default = intersect)</td>
<td style="width:100px;">STRING</td></tr>
<tr><td></td><td colspan=2><table border=0 cellpadding=0 align="center" width="100%">
<tr><td colspan=3>No parameters for selection "intersect"</td></tr>
<tr><td colspan=3>No parameters for selection "union"</td></tr>
<tr><td colspan=3>Parameters for selection "intermediate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr><td colspan=3>Parameters for selection "annotate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
</table></td></tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar merge g=<GeMoMa> GeMoRNA=<GeMoRNA>

GeMoSeq

2024-11-08T16:19:18Z

Grau: /* Analyzer */

GeMoSeq

2024-11-08T16:19:07Z

Grau: /* GeMoMa Annotation Filter */

== Tools ==

=== GeMoRNA ===

''GeMoRNA'' may be called with

java -jar GeMoRNA-1.0.jar gemorna

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna,fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mapped reads (Mapped Reads in BAM format, coordinate sorted, type = bam)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>s</td>
<td>Stranded (Library strandedness, range={FR_UNSTRANDED, FR_FIRST_STRAND, FR_SECOND_STRAND}, default = FR_UNSTRANDED)</td>
<td style="width:100px;">STRING</td>
</tr>
<tr style="vertical-align:top">
<td>l</td>
<td>Longest intron length (Length of the longest intron reported, default = 100000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>sil</td>
<td>Shortest intron length (Length of the shortest intron considered, default = 10)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>lr</td>
<td>Long reads (Long-read mode, default = false)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
<tr style="vertical-align:top">
<td>mnor</td>
<td>Minimum number of reads (Minimum number of reads required for an edge in the read graph, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfor</td>
<td>Minimum fraction of reads (Minimum fraction of reads relative to adjacent exons that must support an intron in the enumeration, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mnoir</td>
<td>Minimum number of intron reads (Minimum number of reads required for an intron, default = 1.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mfoir</td>
<td>Minimum fraction of intron reads (Minimum fraction of reads relative to adjacent exons for an intron to be considered, default = 0.01)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>Percent explained (Percent of abundance that must be explained by transcript models after quantification, default = 0.9)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpg</td>
<td>Minimum reads per gene (Minimum abundance required for a gene to be reported, default = 40.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrpt</td>
<td>Minimum reads per transcript (Minimum abundance required for a transcript to be reported, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>pa</td>
<td>Percent abundance (Minimum relative abundance required for a transcript to be reported, default = 0.05)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>sf</td>
<td>Successive fraction (Factor of the drop in abundance between successive transcript models, default = 20.0)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
<tr style="vertical-align:top">
<td>mrl</td>
<td>Maximum region length (Maximum length of a region considered before it is split, default = 750000)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mfgl</td>
<td>Maximum filled gap length (Maximum length of a gap filled by dummy reads, default = 50)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>q</td>
<td>Quality filter (Minimum mapping quality required for a read to be considered, default = 40)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>mpl</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
<tr style="vertical-align:top">
<td>threads</td>
<td>The number of threads used for the tool, defaults to 1</td>
<td>INT</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar gemorna g=<Genome> m=<Mapped_reads>

=== Predict CDS from GFF ===

''Predict CDS from GFF'' may be called with

java -jar GeMoRNA-1.0.jar predictCDS

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>Genome (Genome sequence as FastA, type = fa,fna.fasta)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>predicted annotation ("GFF or GTF file containing the predicted annotation", type = gff,gff3,gff.gz,gff3.gz,gtf,gtf.gz)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Minimum protein length (Minimum length of protein in AA, default = 70)</td>
<td style="width:100px;">INT</td>
</tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar predictCDS g=<Genome> p=<predicted_annotation>

=== Analyzer ===

This tools allows to compare true annotation with predicted annotation as it is frequently done in benchmark studies. Furthermore, it can return a detailed table comparing true annotation and predicted annotation which might help to identify systematical errors or biases in the predictions. Hence, this tool might help to detect weaknesses of the prediction algorithm.

True and predicted transcripts are evaluated based on nucleotide F1 measure. For each predicted transcript, the true transcript with highest nucleotide F1 measure is listed. A negative value in a F1 measure column indicates that there is a predicted transcript that matches the true transcript with a F1 measure value that is the absolute value of this entry, but there is another true transcript that matches this predicted transcript with an even better F1. Also true and predicted transcripts are listed that do not overlap with any transcript from the predicted and true annotation, respectively. The table contains the attributes of the true and the predicted annotation besides some additional columns allowing to easily filter interesting examples and to do statistics.

The evaluation can be based on CDS (default) or exon features. The tool also reports sensitivity and precision for the categories gene and transcript.

For more information please visit http://www.jstacs.de/index.php/GeMoMa
If you have any questions, comments or bugs, please check FAQs on our homepage, our github page https://github.com/Jstacs/Jstacs/labels/GeMoMa or contact jens.keilwagen@julius-kuehn.de

''Analyzer'' may be called with

java -jar GeMoRNA-1.0.jar Analyzer

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>t</td>
<td>truth (the true annotation, type = gff,gff3,gtf,gff.gz,gff3.gz,gtf.gz)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr><td colspan=3>The following parameter(s) can be used multiple times:</td></tr>
<tr><td></td><td colspan=2><table border=0 cellpadding=0 align="center" width="100%">
<tr style="vertical-align:top">
<td>n</td>
<td>name (can be used to distinguish different predictions, OPTIONAL)</td>
<td style="width:100px;">STRING</td>
</tr>
<tr style="vertical-align:top">
<td>p</td>
<td>predicted annotation (GFF/GTF file containing the predicted annotation, type = gff,gff3,gtf,gff.gz,gff3.gz,gtf.gz)</td>
<td style="width:100px;">FILE</td>
</tr>
</table>
</td></tr>
<tr style="vertical-align:top">
<td>c</td>
<td>CDS (if true CDS features are used otherwise exon features, default = true)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
<tr style="vertical-align:top">
<td>o</td>
<td>only introns (if true only intron borders (=splice sites) are evaluated, default = false)</td>
<td style="width:100px;">BOOLEAN</td>
</tr>
<tr style="vertical-align:top">
<td>w</td>
<td>write (write detailed table comparing the true and the predicted annotation, range={NO, YES}, default = NO)</td>
<td style="width:100px;">STRING</td></tr>
<tr><td></td><td colspan=2><table border=0 cellpadding=0 align="center" width="100%">
<tr><td colspan=3>No parameters for selection "NO"</td></tr>
<tr><td colspan=3>Parameters for selection "YES":</td></tr>
<tr style="vertical-align:top">
<td>ca</td>
<td>common attributes (Only gff attributes of mRNAs are included in the result table, that can be found in the given portion of all mRNAs. Attributes and their portion are handled independently for truth and prediction. This parameter allows to choose between a more informative table or compact table., valid range = [0.0, 1.0], default = 0.5)</td>
<td style="width:100px;">DOUBLE</td>
</tr>
</table></td></tr>
<tr style="vertical-align:top">
<td>r</td>
<td>reliable (additionally evaluate sensitivity for reliable transcripts, range={NO, YES}, default = NO)</td>
<td style="width:100px;">STRING</td></tr>
<tr><td></td><td colspan=2><table border=0 cellpadding=0 align="center" width="100%">
<tr><td colspan=3>No parameters for selection "NO"</td></tr>
<tr><td colspan=3>Parameters for selection "YES":</td></tr>
<tr style="vertical-align:top">
<td>f</td>
<td>filter (A filter for deciding which transcript from the truth are reliable or not. The filter is applied to the GFF attributes of the truth. You probably need to run AnnotationEvidence on the truth GFF. The default filter decides based on the completeness of the prediction (start=='M' and stop=='*'), no premature stop codons (nps==0), RNA-seq coverage (tpc==1) and intron evidence (isNaN(tie) or tie==1)., default = start=='M' and stop=='*' and nps==0 and (tpc==1 and (isNaN(tie) or tie==1)), OPTIONAL)</td>
<td style="width:100px;">STRING</td>
</tr>
</table></td></tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar Analyzer t=<truth> p=<predicted_annotation>

=== Merge ===

''Merge'' may be called with

java -jar GeMoRNA-1.0.jar merge

and has the following parameters

<table border=0 cellpadding=10 align="center" width="100%">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr style="vertical-align:top">
<td>g</td>
<td>GeMoMa (GeMoMa predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA</td>
<td>GeMoRNA (GeMoRNA predictions, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>m</td>
<td>Mode (, range={intersect, union, intermediate, annotate}, default = intersect)</td>
<td style="width:100px;">STRING</td></tr>
<tr><td></td><td colspan=2><table border=0 cellpadding=0 align="center" width="100%">
<tr><td colspan=3>No parameters for selection "intersect"</td></tr>
<tr><td colspan=3>No parameters for selection "union"</td></tr>
<tr><td colspan=3>Parameters for selection "intermediate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr><td colspan=3>Parameters for selection "annotate":</td></tr>
<tr style="vertical-align:top">
<td>GeMoMa-strict</td>
<td>GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
<tr style="vertical-align:top">
<td>GeMoRNA-strict</td>
<td>GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3)</td>
<td style="width:100px;">FILE</td>
</tr>
</table></td></tr>
<tr style="vertical-align:top">
<td>outdir</td>
<td>The output directory, defaults to the current working directory (.)</td>
<td>STRING</td>
</tr>
</table>

'''Example:'''

java -jar GeMoRNA-1.0.jar merge g=<GeMoMa> GeMoRNA=<GeMoRNA>