GeMoRNA: Difference between revisions
No edit summary |
No edit summary |
||
Line 3: | Line 3: | ||
It is intended as a companion for the homology-based gene prediction program [[GeMoMa]]. | 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. | 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. | ||
Latest revision as of 16:34, 8 November 2024
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 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 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 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
name | comment | type |
g | Genome (Genome sequence as FastA, type = fa,fna,fasta) | FILE |
m | Mapped reads (Mapped Reads in BAM format, coordinate sorted, type = bam) | FILE |
s | Stranded (Library strandedness, range={FR_UNSTRANDED, FR_FIRST_STRAND, FR_SECOND_STRAND}, default = FR_UNSTRANDED) | STRING |
l | Longest intron length (Length of the longest intron reported, default = 100000) | INT |
sil | Shortest intron length (Length of the shortest intron considered, default = 10) | INT |
lr | Long reads (Long-read mode, default = false) | BOOLEAN |
mnor | Minimum number of reads (Minimum number of reads required for an edge in the read graph, default = 1.0) | DOUBLE |
mfor | Minimum fraction of reads (Minimum fraction of reads relative to adjacent exons that must support an intron in the enumeration, default = 0.01) | DOUBLE |
mnoir | Minimum number of intron reads (Minimum number of reads required for an intron, default = 1.0) | DOUBLE |
mfoir | Minimum fraction of intron reads (Minimum fraction of reads relative to adjacent exons for an intron to be considered, default = 0.01) | DOUBLE |
p | Percent explained (Percent of abundance that must be explained by transcript models after quantification, default = 0.9) | DOUBLE |
mrpg | Minimum reads per gene (Minimum abundance required for a gene to be reported, default = 40.0) | DOUBLE |
mrpt | Minimum reads per transcript (Minimum abundance required for a transcript to be reported, default = 20.0) | DOUBLE |
pa | Percent abundance (Minimum relative abundance required for a transcript to be reported, default = 0.05) | DOUBLE |
sf | Successive fraction (Factor of the drop in abundance between successive transcript models, default = 20.0) | DOUBLE |
mrl | Maximum region length (Maximum length of a region considered before it is split, default = 750000) | INT |
mfgl | Maximum filled gap length (Maximum length of a gap filled by dummy reads, default = 50) | INT |
q | Quality filter (Minimum mapping quality required for a read to be considered, default = 40) | INT |
mpl | Minimum protein length (Minimum length of protein in AA, default = 70) | INT |
outdir | The output directory, defaults to the current working directory (.) | STRING |
threads | The number of threads used for the tool, defaults to 1 | INT |
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
name | comment | type |
g | Genome (Genome sequence as FastA, type = fa,fna.fasta) | FILE |
p | predicted annotation ("GFF or GTF file containing the predicted annotation", type = gff,gff3,gff.gz,gff3.gz,gtf,gtf.gz) | FILE |
m | Minimum protein length (Minimum length of protein in AA, default = 70) | INT |
outdir | The output directory, defaults to the current working directory (.) | STRING |
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
name | comment | type | ||||||||||||||||||||||||
g | GeMoMa (GeMoMa predictions, type = gff,gff3) | FILE | ||||||||||||||||||||||||
GeMoRNA | GeMoRNA (GeMoRNA predictions, type = gff,gff3) | FILE | ||||||||||||||||||||||||
m | Mode (, range={intersect, union, intermediate, annotate}, default = intersect) | STRING | ||||||||||||||||||||||||
| ||||||||||||||||||||||||||
outdir | The output directory, defaults to the current working directory (.) | STRING |
Example:
java -jar GeMoRNA-1.0.jar merge g=<GeMoMa> GeMoRNA=<GeMoRNA>