Mercurial > repos > ldelisle > revertr2orientationinbam

diff revertR2orientationInBam/.shed.yml @ 0:07695b197e6c draft

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author ldelisle
date Wed, 19 Oct 2022 08:30:26 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revertR2orientationInBam/.shed.yml	Wed Oct 19 08:30:26 2022 +0000
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+categories:
+   - SAM
+description: Revert the mapped orientation of R2 mates in a bam.
+name: revertr2orientationinbam
+owner: lldelisle
+long_description: This tool is very useful when you have paired-end stranded RNA-seq. Using this tool prior to a bedtools genome coverage allow to have strand specific coverage using both mates. It uses samtools to convert input to sam format and then awk to modify the flag "reverse strand" for the second mate of pairs.