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ron128 / chimerascan

Automatically exported from code.google.com/p/chimerascan
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Improve localization of 5' and 3' exons #3

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Use mismatch information (e.g. the MD tag in SAM) to trim read alignments that 
have mismatches in the first/last bases.  This splash occurs when aligning 
chimeric reads that span a junction by <= 2 bases (or the number of allowed 
mismatches in the alignment tool).

Trim the beginning/end of the joined reads to eliminate these leading/trailing 
mismatches and improve alignment. 

Current solution is to simple add/subtract 2 from read alignments during 
chimera nomination phase.

Original issue reported on code.google.com by matthew....@gmail.com on 17 Jan 2011 at 6:55

GoogleCodeExporter commented 8 years ago 
No longer applicable as new version now uses bowtie2 local alignment to align 
breakpoint-spanning reads

Original comment by matthew....@gmail.com on 11 Sep 2012 at 6:33