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Old 03-01-2012, 06:53 AM   #1
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Location: Philadelphia

Join Date: Feb 2012
Posts: 9
Default Anyone has experience with Bowtie2?

Hi All,
my name is Lucia, and I've been lurking around for a while but this is my first post.
I have a pretty big ChIP-seq experiment to analyze, and initially did the alignments with Bowtie. The stats were not that great, and since I have 100bp reads, I decided to redo the alignments with Bowtie2
I do get a lot more mapped reads, but the quality scores seem a lot lower
The programs compute the scores differently, so I am not sure if the scores are really "lower".
Does Bowtie2 increase mapping at the expense of quality?
Or is the scoring scheme so completely different that the quality scores are not comparable at all?
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