On Sep 21, 2011, at 8:47 AM, shamsher jagat 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?
> 
> 

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



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