SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Indexing ChIPseq libraries using Illumina's TruSeq and ChIPseq kits Alex Clop Epigenetics 6 11-08-2012 11:07 AM
Convert WIG file into Fasta file kumardeep Bioinformatics 3 08-23-2012 04:56 AM
wig file generated by MACS doesn`t fit input sam tujchl Bioinformatics 2 06-16-2011 12:23 AM
18bp DNA contaminant in ChIP input sample? sinapius Sample Prep / Library Generation 0 02-09-2011 11:39 AM
WIG input file for CEAS (Cis-regulatory Element Annotation System) clariet Bioinformatics 3 04-09-2010 07:31 AM

Reply
 
Thread Tools
Old 07-25-2012, 04:10 AM   #1
abmmki
Junior Member
 
Location: Africa

Join Date: Nov 2009
Posts: 5
Question ChIPseq wig file with the input subtracted from ChIP sample

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 BED files for both ChIP and Control. I would like to have one WIG file where input is subtracted already. Any one knows any simple tool/script/method. (except SPP)
abmmki is offline   Reply With Quote
Old 08-02-2012, 05:51 PM   #2
captainentropy
Member
 
Location: San Francisco Bay Area

Join Date: Mar 2009
Posts: 89
Default

GenPlay can do that.

http://genplay.einstein.yu.edu/wiki/...ial&oldid=1373

I think bedtools (subtractBed) can as well but your files have to be BED/GFF format first. You can convert the output to a bedgraph and that can be converted to a wig using tools from UCSC https://groups.google.com/forum/?fro...ss/3CibmlqIdWA

I'm sure there's other tools that I'm not aware of too.
captainentropy is offline   Reply With Quote
Reply

Tags
wig chip-seq count-data

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO