Is there a way to make just one wig file with the input subtracted from ChIP sample? I mean I have a ChIPseq data read aligned BW files for both ChIP(GSM947528) and Input(GSM947411). I would like to have one WIG file where input is subtracted already. Any one knows any simple method.
thanks
Fujun
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qinfujun •
1 answer
MACS2 can be used to calculate the fold enrichment or logLR between treatment and input samples generated using Chip-seq.
https://github.com/taoliu/MACS/
MACS2 generates the begraph files. You can use UCSC tools (bdg2bw) to generate the bigwig files containing fold enrichment or logLR values.
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig
You can check the detailed commands for this protocol in the following link
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Hello GANI,
I hope you answer this as I know your post was for 15 months ago!
I was wondering if you can take GSM947411 as input for GSM947528?
If so would it be possible to use GSM947411 for GSM947524 as well? I want to do peak calling!
I wanted to do differential peak calling between healthy and cancer data, apparently I cannot use cancer data (GSM947524) and assume the healthy sample ([GSM947523]2]) as control to do peak calling with MACS! but rather I need two do separate peak calling for healthy and cancerous?
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