Chipseq Wig File With Input Subtracted From Chip Input

Question

[qinfujun]

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

[ukpersia1]

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?

BEST REGARDS

Answer 1

[GANI]

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

https://github.com/taoliu/MACS/wiki/Build-Signal-Track