GeMoRNA: Difference between revisions

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== Tools ==


=== GeMoRNA ===
== GeMoRNA ==


Prediction of transcript models using GeMoRNA.




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=== Predict CDS from GFF ===
== Predict CDS from GFF ==


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




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=== Merge ===
== Merge ==
 


Merging GeMoRNA and GeMoMa predictions.


''Merge'' may be called with
''Merge'' may be called with

Revision as of 16:21, 8 November 2024

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
No parameters for selection "intersect"
No parameters for selection "union"
Parameters for selection "intermediate":
GeMoMa-strict GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3) FILE
GeMoRNA-strict GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3) FILE
Parameters for selection "annotate":
GeMoMa-strict GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3) FILE
GeMoRNA-strict GeMoRNA-strict (GeMoRNA predictions with strict settings, type = gff,gff3) FILE
outdir The output directory, defaults to the current working directory (.) STRING

Example:

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