Question: bigwig to peak
1
gravatar for Nicolas Rosewick
4.8 years ago by
Belgium, Brussels
Nicolas Rosewick7.5k wrote:

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

bigwig chip-seq peak • 7.2k views
ADD COMMENTlink modified 3 months ago by liruiradiant10 • written 4.8 years ago by Nicolas Rosewick7.5k

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

ADD REPLYlink modified 3 months ago • written 3 months ago by liruiradiant10
5
gravatar for Ming Tang
4.8 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

MACS2 can call peak from bedgraph, you can convert bigwig to bedgraph first by bigwigtobedgraph from here http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/  and then call peak with MACS2 https://github.com/taoliu/MACS/

bdgpeakcall: Call peaks from bedGraph output.
ADD COMMENTlink written 4.8 years ago by Ming Tang2.5k

thanks that's perfect

ADD REPLYlink written 4.8 years ago by Nicolas Rosewick7.5k

thanks that's perfect

ADD REPLYlink written 4.8 years ago by Nicolas Rosewick7.5k
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