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Old 04-04-2016, 05:48 AM   #1
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Location: NYC

Join Date: Apr 2016
Posts: 4
Default Bowtie (Bismark) 100% of reads fail to align

I am using bismark in order to observe the progression of methylation on specific CpG sites of different viral variants. One of the steps of bismark is to use Bowtie in order to align paired end reads to a CT converted reference genome. At this step all reads fail to align. This is strange since the issue is isolated to this single variant. I also aligned all of the reads for this variant to a CT converted version of the reference genome with BWA and all of the reads align at the expected position. Is this due to bowtie masking the reads because of low complexity. Or is there something else that is different between BWA and bowtie that is causing the issue?

Using bowtie just to align reads to the converted reference yields the same alignment error. I also tried playing with the options in bowtie to allow more mismatches and increase the insertion size, but the same failure persists.
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