Question: Chipseq Wig File With Input Subtracted From Chip Input
0
gravatar for qinfujun
5.3 years ago by
qinfujun0
qinfujun0 wrote:

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

• 2.0k views
ADD COMMENTlink modified 5.3 years ago by GANI220 • written 5.3 years ago by qinfujun0

Hello GANI,

I hope you answer this as I know your post was for  15 month 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) as control to do peak calling with MACS! but rather I need two do separate peak calling for healthy and cancerous? 

BEST REGARDS

 

ADD REPLYlink written 4.0 years ago by ukpersia1 20
0
gravatar for GANI
5.3 years ago by
GANI220
United States
GANI220 wrote:

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

ADD COMMENTlink written 5.3 years ago by GANI220
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1859 users visited in the last hour