bigwig to peak

Question

[Nicolas Rosewick]

Hi,

I've a bigwig containing a chip-seq signal for a histone mark (H3K4me1) and I want to produce a bed file containing the peaks (the same way MACS produced a bigwig and a peak bed file)? How can I do that? If it's impossible I can realign the raw data and do the whole peak calling step but I prefer to avoid that.

Thanks

[liruiradiant]

I ran into the same goal. However, I believe this is not working, as the bigwig might not be properly normalized the way that MACS does it

Answer 1

[Ming Tommy Tang]

MACS2 can call peak from bedgraph, you can convert bigwig to bedgraph first by bigwigtobedgraph from here and then call peak with MACS2.

bdgpeakcall: Call peaks from bedGraph output.

[Nicolas Rosewick]

thanks that's perfect