GeMoRNA
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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>
