That is correct, I was able to standardize the work flow, which can be a starting point for others. I can add to Galaxy shared addition, so that others may not waste time in looking at what I was searching (at least). Thanks On Tue, Aug 7, 2012 at 12:59 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

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<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 details, follow the documentation links on Galaxy's SICER tool form to reach the primary documentation and tool author's direct help for how to interpret/understand the various outputs.

There are no community contributed SICER tutorials/pages/workflows (that I am aware of, please correct me!), but if developed, I am sure this would be a welcomed addition to the "Shared" content on Galaxy Main or galaxyproject.org.

Best,

Jen Galaxy team

On 7/10/12 3:52 PM, shamsher jagat wrote:

...

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 8. test w200-G600 FDR.05 score island 9. test w200-G600 summary island

Which of these files should be used. I think file 5 and 6 are the ones for visualization as well for annotating with genomic regions. I have read the original paper but it is not very clear what these out puts mean. Could some one please guide me what these files mean and what is useful and rest are intermediate files.

My second question is authors of SICER has emphasized about teh importance of choosing gap size and window size. gap size they mention 1-3 -5 depending upon the peak distribution, but I see in Galaxy the default is 600 gap size do we need to change it to 1,2- 5 or I am missing something.

Any advise please but I did my searching on net.

Thanks

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