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This analysis lets you find peaks that are distant enough from known genes. This can be useful to find distal enhancers, etc.
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. To find peaks that are more than 5kb away from any genes (RefSeq), type the following command:
ChIPseeqerFindDistalPeaks --peakfile=TF_targets.txt --mindistaway=5000
The following options are available:
--peakfile=FILE file containing genomic regions --prefix=STR prefix for output files --mindistaway=INT minimum distance away from transcripts. Default is 5000bp --genome=STR can be hg18 (human), mm9 (mouse), dm3 (drosophila), or sacser (for Saccharomyces cerevisiae) --db=STR can be refSeq (available for hg18, mm9, dm3), AceView (for hg18, mm9), Ensembl (for hg18, mm9, dm3) UCSCGenes (for hg18, mm9). Default is refSeq.
IMPORTANT: Note that in the --peakfile option you must enter the ChIPseeqer output file.
2. See the results.
The output of this process are 2 files with the extensions: .DISTPEAKS (contains distal peaks) and .GENEPEAKS (contains peaks within genes - or within mindistaway of genes)
3. What can I do next ?
- Evaluate whether these distal peaks are more conserved than random peaks. This is explained in Elementolab/ChIPseeqer_Evaluating_Conservation_Of_Distal_Peaks
- Determine which of these peaks overlap (or don't overlap) with other peaks obtained from other ChIP-seq experiments. This is explained in Elementolab/Compare_Intervals
- Find the genes that are closest to these peaks. This is explained in Elementolab/ChIPseeqerFindClosestGenes