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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Q: Can I use bigWig data for peak calling? #525

Open jdmontenegro opened 2 years ago

jdmontenegro commented 2 years ago

Hi,

I have access to bigWig file from an ATACseq experiment, but I do not have the original fastqs nor the bam files of the alignment. I wanted to know if there is a way to identify peaks from this data.

I have converted the bigWig to bedgraph and used "bdgpeakcall" on it, but the assumption of bdgpeakcall is that the input bedgraph was generated by macs, which I don't think is the case for this file.

How can I find ideal parameters for background noise and identify significant peaks from this data? I look forward to hearing back from you.

Kind regards,

Juan D. Montenegro

jiangshan529 commented 2 years ago

same question, please let me know if they respond or if you figure it out.

taoliu commented 2 years ago

@jdmontenegro @jiangshan529 Simple solution is to download the bigWigToBedGraph tool from UCSC: https://hgdownload.soe.ucsc.edu/admin/exe/. Then convert the bigwig to bedgraph, then use bdgpeakcall.