Back to Elementolab/ChIPseeqer_Tutorial
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.
In this analysis you can get the average or maximum reads count for each peak.
The input of this script is the peaks file created after running run ChIPseeqer.
1. To run the script type the command:
ChIPseeqerGetReadCountInPeakRegions -intervals peaks.txt -chipdir CHIP/ -chrdata DATA/hg18.chrdata -outfile out.txt -desc desc
Available options are:
-intervals FILE file containing the peaks -hasid INT use 1 if intervals have id in first column -chipdir DIR directory that contains the ChIP reads (one file per chromosome, named reads.chr1, reads.chr2, etc). -chrdata STR to run for organisms other that human (default is hg18), point to files: DATA/mm9.chrdata for mouse, DATA/dm3.chrdata for drosophila or DATA/sacser.chrdata for Saccharomyces cerevisiae -outfile STR indicates the output file (provide full path) -output STR can be either max or avg and indicates the average or maximum reads count for each peak. Default is set to avg. -normalize INT set to 1 in order to normalize the counts -ext INT the extension of the peaks. Default is set to 0. -format STR format of the read files: sam, mit, bed, eland. Default is eland. -desc STR description to be included in header
There's another set of options to directly extract read counts from promoter regions or transcription end sites of RefSeq transcripts.
-tsregion STR TSS or TES -refgene FILE refGene (e.g. DATA/hg18/refGene.txt.07Jun2010) -up INT how many bp upstream of TSS (or TES) -dn INT how many bp downstream of TSS (or TES)
2. See the results.
The results will be similar to the input peaks file with the last column indicating the avg or max reads count (based on the option used).
chrY 57405212 57406043 -20.6441 12.6398 57405522 16 37.3 831 57405627 105 1.261 chrY 57406324 57406626 -22.7798 13.6534 57406464 20 46.2 302 57406475 11 1.671 chrY 57411159 57412052 -25.6472 15.0509 57411925 20 85.7 893 57411605 320 1.723 chrY 57412321 57413102 -27.1784 15.7997 57412641 21 40.9 781 57412711 70 2.027 chrY 57415332 57415537 -21.8731 13.2513 57415421 16 43.2 205 57415434 13 1.865 chrY 57427854 57427998 -17.4823 11.0448 57427982 13 88.3 144 57427926 56 1.419