I am doing ChIP-Seq analysis, I already have done the peak calling and obtained the BED and WIG files of my peaks. Now I want to retrieve 50 bases around the summit of the peaks in FASTA file. I found that PeakAnalyzer does it but does not contain the Vibrio cholera genome, which is the bacteria I work with. I would like to call subpeaks within my peak file since I have used MACS on galaxy and SeqMonk to do the peak calling but the result is always that peaks that are close are called as a single one.
Does anybody know a nice software that does not require command line and run in window with a GUI?
You can go for AVADIS NGS
http://www.avadis-ngs.com/
as you have done most of your work already the free trial should be sufficient for your next part of analysis.
So your peaks are in bed file and you want 50 bases upstream
Step1. extend 50 bps around your peaks if fourth coloumn is strand information
awk '{ if ($4=="+") {print $1, $2-50, $2} else $1, $3, $3+50 }' OFS="\t" your_peaks.bed > upstream.bed
just fetch fasta from your upstrem.bed
bedtools getfasta-fi -bed -fo
Same you can do for downstream just know which coloumn to play with
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