Hi Kanwar,
I found that you also posted this question and another like to the
Google group for SICER on 7/10 and received some help there:
http://groups.google.com/group/sicer-users
Glad that you were able to get the questions resolved. For others
reading this post or interested in SICER
I used SICR to call peaks and have following out put files:
1. test.1removed bed
2. control1 removed .bed
3. test w 200 graph
4. test w200 normalized graph
5. test w200-G600 FDR.05 island.bed
6. test w200-G600 FDR .05 island filtered.bed
7. test w200-G600 FDR .05 island filtered normalized.wig
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