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
MACS2 can call peak from bedgraph, you can convert bigwig to bedgraph first by bigwigtobedgraph from [here][1] and then call peak with [MACS2][2].

>     bdgpeakcall: Call peaks from bedGraph output.

 [1]: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
 [2]: https://github.com/taoliu/MACS/