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Old 04-22-2012, 10:25 PM   #1
nguyendofx
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Location: CA

Join Date: May 2011
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Default BWA vs Novoalign for ChiP Seq

Hello ChiP Seq experts,

1. BWA vs Novoalign, which one is better aligner for ChiP-Seq Application (illumina seq) ?

2. I aligned illumina sequences (100 bp, Single-end reads) with BWA and novoalign (defaul options), bwa yielded 10% more reads mapped than novoalign. Does bwa more specific ? better aligner?

Thanks,
Ng
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