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Old 01-21-2014, 07:28 AM   #1
Jerry_Zhao
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Location: Philadelphia

Join Date: Feb 2012
Posts: 20
Question Bowtie1 for ChIP-seq: uniquely mapped reads with up to two mismatches

Hi All,

I am using Bowtie 1 (0.12.7) to map ChIP-seq reads to mouse genome.

I am trying to only report the uniquely mapped reads with two or less mismatches.
The options I used is "-v 2 -m 1".
Are these options correct?


Many thanks!

Best,
Jerry
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