pyGTF2bed

pyGTF2bed is part of the pyCRAC package. Converts GTF files to the bed 6 format. Gene names present in the GTF file will be included in the bed file.

Parameter list

These options can be used to add and modify a track line for the UCSC genome browser:

--track
                    Use this flag to add a UCSC genome browser track line
                    to the beginning of your file
-n NAME, --name=NAME
                    For the USCS track line: provide a track name. Default
                    = 'User_supplied_track'
-d DESCRIPTION, --description=DESCRIPTION
                    For the USCS track line: provide a track description.
                    Default = 'User_supplied_track'
-c COLOR, --color=COLOR
                    select the track color. Default = black
-s STRANDS, --colorstrands=STRANDS
                    select the colors for each strand. Default =
                    'red,blue'

File input options:

--gtf=Yourfavoritegtf.gtf
                    type the path to the gtf file that you want to
                    convert. Default is standard input