bigwig to peak
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6.8 years ago

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

chip-seq bigwig peak • 15k views
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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

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6.8 years ago
Ming Tang ★ 2.6k

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.
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thanks that's perfect

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thanks that's perfect

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