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
[Bioc-devel] mapToAlignments_issue
2 messages · David Porubsky, James W. MacDonald
This email server is for package development questions. Please direct your question to the support site instead, at support.bioconductor.org -----Original Message----- From: Bioc-devel <bioc-devel-bounces at r-project.org> On Behalf Of David Porubsky Sent: Wednesday, August 03, 2022 1:49 PM To: bioc-devel at 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 _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel