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
Options
- -upstream nrbases
- if nrbases > 0 upstream and downstream regions will
be added, where nrbases gives how many bases will be
assigned as upstream/downstream (default 0)
- -nocds 0/1
- if 1 (default = 0) indications of cdsStart and cdsEnd are not
taken into account, and all genes will be handled as non coding,
meaning that also for coding genes all regions will be output as
type RNA instead of UTR and CDS, and exons containf start or stop
site are in one (RNA) region.
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