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Old 03-01-2012, 07:05 AM   #2
Location: USA

Join Date: Jan 2012
Posts: 38

Sorry can't help you with your specific problem.

Though in my experience, bowtie works much better than bowtie2. Apart from some bugs, many options are missing (strata/unique alignments). I shared my opinion with authors as well.
Must mention that I have 50bp reads and my final goal (ChIP-Seq) may be different from you.
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