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 <j...@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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> --
> Jennifer Jackson
> http://galaxyproject.org
>
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