Man page - bed2sga(1)

Packages contains this manual

Package: chip-seq
apt-get install chip-seq

Manuals in package:

Documentations in package:

bed2sga - Convert BED format into SGA format.

bed2sga [ options ] [ -s <s_assembly (e.g. hg19)> ] [ < ] <BED file|stdin>

- version 1.5.5 where options are:

-d |--debug

Produce Debug information

-h |--help

Show this Help text

-i |--db <path>

Use <path> to locate the assembly-specific chr_NC_gi file [default is: $HOME/db/genome]

-f |--feature <ft>

Set Feature name <ft>

-s |--species <spec>

Assembly <spec> (i.e hg19)

-c |--center

Generate a Centered SGA file

-u |--unoriented

Generate an unoriented SGA file

-r |--regional

Generate a 2-line[+/-] SGA file representing BED regions (e.g. RepeatMasker regions)

-e |--extend <f1,f2,...>

Produce an extended SGA file with additional fields specified by a comma-separated list of BED column numbers (from 1 to n)

--useScore

Use the BED ’score’ field (#5) to set the SGA ’count’ field

--useSigVal

Use the BED ’Signal Value’ field (#7) to set the SGA ’count’ field [This option is only valid for ENCODE narrowPeak]

--narrowPeak

Use this option for ENCODE narrowPeak format [Options --useScore , -c , and -u are ignored]

Convert BED format into SGA format.

This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.