GenomeComb

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Supplementary Data Reumers, De Rijk et al

Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

gene2reg

Format

cg gene2reg ?infile? ?outfile?

Summary

Extract gene elements from data in genepred-like format to a (tab separated) region file.

Description

cg gene2reg outputs a tsv file with the location and meta info about each element of a gene on a separate line. The output is a region file (fields chromosome, begin, end) that typically includes the following extra fields:

type

UTR, CDS, intron, RNA

element

exon1, intron1, exon2, intron1, ...

rna_start

start of the element on the RNA sequence

rna_end

end of the element on the RNA sequence

protein_start

start of the element on the RNA sequence relative to the protein start

protein_end

start of the element on the RNA sequence relative to the protein start

gene

gene name

transcript

transcript id

Arguments

infile

file to be converted, if not given, uses stdin. File may be compressed.

outfile

write results to outfile, if not given, uses stdout

Category

Format Conversion