bed2bed_display - Convert BED file to BED format suitable for
displaying ChIP-seq peaks.
bed2bed_display [options] [-a <min BED
score>] [-b <max BED score>] [<] <BED
file|stdin>
- - version 1.5.5 where options are:
- -d|--debug
- Produce Debug information
- -h|--help
- Show this Help text
- -f|--feature
<ft>
- Set Feature name <ft>
- -o|--oformat
<1|2>
- Set output Format (1:BED[Def] 2:BedGraph)
- --name
<name>
- Set name for track name field [def. name=SGA-feature]
- --desc
<desc>
- Set track description field [def. desc="ChIP-Seq Custom
data"]
- --color
<col>
- Define the track color in comma-separated RGB values [def.
100,100,100]
- --autoscale
- <on|off> Data viewing paramenter: set auto-scale to UCSC data view
[def=OFF]
- --always0
- <on|off> Data viewing paramenter: always include zero [def=OFF]
- --wfunction
- <func> Data viewing paramenter: windowing function
[def=mean+whiskers|maximum|mean|minimum]
- --smoothing
- <grade> Data viewing paramenter: smoothing window [def=OFF[0],
<grade>=0,2..16]
- --visibility
<mode>
- Display mode: [def=dense|full|hide] or [def=1|2|3]
- Convert BED file to BED format suitable for displaying ChIP-seq peaks. Two
formats are supported: 1) BED Track with Score field; 2) BedGraph. For BED
track format, only the graphical parameter 'visibility' can be set.
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.