Hi
I need to determine average coverage in ChiP-seq peaks. I tried to use bedtools multicov with sorted bam-file with mapped reads and bed-file with peaks. Default minimum overlap of a read and a peak is 1 bp. What minimum overlap (in percent) should I use?
Thanks for the explanation. I have one more question, if I have narrowPeak file from ENCODE (SPP might be used to call peaks), how can I get the tag density or binding affinity in the peak region?
The format description is here: http://genome.ucsc.edu/FAQ/FAQformat.html#format12
So field 7 gets you the average enrichment over the peak while field 9 gives the FDR.