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edwardhust / chimerascan

Automatically exported from code.google.com/p/chimerascan
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Improvement when joining segments #2

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Assume for segments 1,2,3,4.  If segment 2 is unmapped due to multimapping the 
joiner will output split reads for segment 1, segment 2, and segments 3-4.  If 
we check segment 2 for the multimapping (XM) tag in bowtie and allow the 
segment joining logic to skip segments, we could potentially recover segment 2 
(infer its position based on the positions of the other segments) and not need 
to report a split.

Original issue reported on code.google.com by matthew....@gmail.com on 15 Jan 2011 at 8:21

GoogleCodeExporter commented 9 years ago 
With chimerascan version 0.4.0, this issue is no longer reflected as segmented 
alignment has changed

Original comment by matthew....@gmail.com on 4 Jul 2011 at 2:28