GeMoRNA

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
	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>