I used SICR to call peaks  and have  following out put files:<div><br></div><div>1. test.1removed bed</div><div>2. control1 removed .bed</div><div>3. test w 200 graph</div><div>4. test w200 normalized graph</div><div>5. test w200-G600 FDR.05 island.bed</div>
<div>6. test w200-G600 FDR .05 island filtered.bed</div><div><div>7. test w200-G600 FDR .05 island filtered normalized.wig</div><div>8. test w200-G600 FDR.05 score island</div><div>9. test w200-G600 summary  island</div><div>
<br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>Any advise please but I did my searching on net.</div><div><br></div><div>Thanks</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><br class="Apple-interchange-newline"></div>
<div><br></div>