James W. MacDonald
jm@cdon @end|ng |rom uw@edu
Wed Aug 3 20:07:04 CEST 2022
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From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of David Porubsky
Sent: Wednesday, August 03, 2022 1:49 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] mapToAlignments_issue
I'm trying to map genome coordinates back to local (contig/read) coordinates, however, I have an issue to do this properly in cases when alignment between contig and the genome (reference) is in minus (reverse) orientation.
Is there a way to use function GenomicAlignments::mapToAlignments in strand aware fashion such that reverse alignments will be mapped in minus orientation?
Is there an example code on how to this properly?
Thank you in advance,
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