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Old 05-08-2011, 12:55 AM   #1
Rachelly
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Location: Israel

Join Date: Oct 2010
Posts: 37
Default Number of mismatches in Bowtie

Hi all,

Bowtie's manual says the following about -v mode:
"-v <int> Report alignments with at most <int> mismatches"

I understood from this that for paired end reads the whole alignment, including both ends, will contain up to <int> mismatches.

But when I ran my data with -v 2 mode I got the following MD:Z values for 2 ends of the same read:
23A3A36
59T3T0

and another example:
32A13G17
15A21A26

So it seems like 2 mismatches are allowed per end.

Just wanted to make sure that this what -v means, and that I didn't do something else that caused this.

Thanks,
Rachelly.
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