ChIP-seq peak calling
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7 days ago
Omnia • 0

Hello, I have ChIP-seq Bigwig files downloaded from NCBI. I want to get (.narrowpeak) files. Is it possible to convert BigWig files to bedgraph files and the use MACS2 to get (.narrowpeak) file format? Thanks for help!

narrow_Peak ENCODE ChIPseq BigWig • 200 views
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Technically this is possible, yes. Still, you often do not know how these files were created and whether macs2 plays well with bedGraphs that were not created by the tool itself internally. I personally would not trust these results. ChIP-seq is already a very noisy experiment. Non-standard processing does not improve things. I would get the raw data if possible and call the peaks, or check whether you can get peaks from the ReMap2022 database which basically has uniformly processed a great many datasets from NCBI, maybe yours is included.

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Thanks a lot for this informative reply. I will check ReMap2022 database.

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