I've got ChIP-seq data analyzed with MACS and looks at such:
> chr start end length summit tags -10log10(pvalue) fold_enrichment FDR(%)
> chr1 9911 10616 706 251 77 60.46 4.07 0.30
> chr1 11119 11740 622 185 32 101.80 10.07 0.13
etc...
How do I now select the relevant peaks according to these scores. I'm looking for a sort of threshold-value for which I can say "Any peak with a score above this value is an actual binding site".
I read the Zhang article already but couldn't find any parameters to use.
Many thanks!
Stijn
•
written
by
robbenstijn •
1 answer
If you have biological replicates, you might want to use MACS2 in combination with the Irreproducible Discovery Rate (IDR) pipeline to identify peaks that are reproducibly detected between your replicates. If you only have a single replicate there is a workaround discussed here, though replicates are highly recommended: https://groups.google.com/forum/#!searchin/idr-discuss/no$20replicates%7Csort:relevance/idr-discuss/edIg7xjism8/B4XsmTQJZRsJ
Log in to answer this question.