Hello Falak, Apologies for the delay in reply. Are you still having issues? Is so, sharing a link to a history that demonstrates the issue would be helpful. You can email the link directly to me if you need to keep your data private. Best, Jen Galaxy team On 4/7/11 9:00 AM, Sher, Falak wrote:

while using MSCS tool from Galaxy I get following mesg. with BED file:

"Treatment tags and Control tags are uneven! FDR may be wrong"

Any suggestion to fix it..

I don't understand its implication, my data is form single illumina chIP-Seq experiment. I use Bowtie from Galaxy for mapping.

F

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