From Icbwiki

Revision as of 19:24, 20 September 2012; view current revision
←Older revision | Newer revision→
Jump to: navigation, search

Back to Elementolab/ChIPseeqer_Tutorial


This analysis helps you create UCSC Genome Browser tracks (WIGL) from the output of ChIPseeqer.

To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH variable. Read How to set the CHIPSEEQERDIR variable.

1. Type the command:

ChIPseeqerPeaksTrack --targets=TF_targets.txt --trackname="TF ChIPseeqer peaks"
--peakfile=FILE File with ChIP-seq peaks.
--trackname=DIR Define the name of the peaks track.
--outfile=STR   Define the name of the output file.

This command will create a gzipped file name TF_targets.txt.wgl.gz.

You can then point your Web browser to UCSC Genome Browser, and upload the track in the "Add custom tracks" section (or "Manage custom tracks").

The black bars that you will see in the Genome Browser will correspond to the ChIPseeqer peaks.

To create a track for GMOD-type genome browsers:

ChIPseeqer2GMODTrack --targets=TF_targets.txt

This command will create a file name TF_targets.txt.gmod.

Personal tools