Question: Chip-Seq
gravatar for shamsher jagat
7.2 years ago by
United States
shamsher jagat590 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 COMMENTlink modified 7.2 years ago by Ido M. Tamir280 • written 7.2 years ago by shamsher jagat590
gravatar for Ido M. Tamir
7.2 years ago by
Ido M. Tamir280
Ido M. Tamir280 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 has also a lot of analysis tools best, ido
ADD COMMENTlink written 7.2 years ago by Ido M. Tamir280
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