[Bioc-devel] mapToAlignments_issue

[James W. MacDonald]

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-----Original Message-----
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

Dear Bioc-team,

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,

David

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