Elementolab/ChIPseeqerGetReadCountInPeakRegions

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ChIPseeqerGetReadCountInPeakRegions

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).

For example,

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