Question: bowtie2 "Pct aligned concordantly >1 times" question
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gravatar for mark.rose
2.4 years ago by
mark.rose30
United States
mark.rose30 wrote:

Hello

Bowtie2 reports on "Pct aligned concordantly >1 times", does that imply that the multiple concordant alignments map equally well?

Thanks

bowtie concordant bowtie2 • 709 views
ADD COMMENTlink modified 2.4 years ago by Devon Ryan89k • written 2.4 years ago by mark.rose30
0
gravatar for Devon Ryan
2.4 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Yes, these alignments are only for concordantly aligned pairs that multimap equally well (and concordantly!) to multiple places. These tend to be low complexity regions, in my experience.

ADD COMMENTlink written 2.4 years ago by Devon Ryan89k

Thanks a lot. In my case they are not low complexity but multicopy regions

ADD REPLYlink written 2.4 years ago by mark.rose30
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