Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Chip-Seq
0
gravatar for shamsher jagat
7.2 years ago by
shamsher jagat • 590
United States
shamsher jagat • 590 wrote:
Can I analyze two bed files from Chip seq experiemnt in Galaxy? I have one file of input and other of sample. Both these files have peak locations. Any suggestion of a work flow in Galaxy?
galaxy • 1.2k views
ADD COMMENT • link •
modified 7.2 years ago by Ido M. Tamir • 280 • written 7.2 years ago by shamsher jagat • 590
0
gravatar for Ido M. Tamir
7.2 years ago by
Ido M. Tamir • 280
Austria
Ido M. Tamir • 280 wrote:
The bed file consists of called peaks done separately? Is there any peak calling done with ChIP vs Input? Or are the bed files location of reads. If the number of lines more than 100000 then its not peak locations but reads. It is very important to do peak calling against an input. You can do this in galaxy if the bed files are reads: NGS: Peak Calling => MACS Otherwise, if you have no other option, you can try subtracting the input peaks from the ip peaks. Operate on Genomic Intervals => Subtract http://cistrome.org/ap/ has also a lot of analysis tools best, ido
ADD COMMENT • link written 7.2 years ago by Ido M. Tamir • 280
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 183 users visited in the last hour