Calling peaks in repeats region ChIP-Seq

[dinodi...@gmail.com]

Hi,

I am performing ChIP-Seq for Candida species. The reference available is at the Supercontig level. 

I had performed the alignment of my 72 bp reads with the reference using Bowtie with parameters -v 3 --best -m1. I called peaks using Homer and obtained peaks exactly where I found enrichment in my PCR. But, except for one Supercontig. I re-did the alignment again with Bowtie using parameter -v3 and nothing else. This time I obtained peaks which were twice as greater in size than the previous alignment (Got peak this time in all Supercontigs). I suspect the Supercontig which did not show enrichement earlier had repeat regions. How do I tackle this issue? What parameters should I give in Bowtie so that I restrict same read aligning at multiple position and also make sure the best alignment is performed as to eliminate false positive results.Any help would be much appreciated.

Thanks,

Kushal

[Anton]

Hi Kushal,

not an expert on Bowtie unfortunately. Perhaps refer to their manual to determine how to output unique best alignment.

Anton