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Saving BWA MEM log #124

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Caffeinated-Code opened this issue Oct 19, 2023 · 0 comments
Open

Saving BWA MEM log #124

Caffeinated-Code opened this issue Oct 19, 2023 · 0 comments
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@edmundmiller
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enhancement New feature or request
Milestone
2.3.0

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@Caffeinated-Code
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Description of feature

The RSeqQC infer_experiment module is quite helpful in deciphering the strandedness of my libraries.
Having the added option to save the bwa mem log will help confirm how the mapper handles these orientations and confidently flip the strands during deeptools bamcoverage step depending on the nascent protocol used - PROseq/PROcap.

Sample of BWA-MEM log showing different orientations.

bwamem

Strand Flipping: Deeptools Bamcoverage

bamcoverage_options

Note: Nice resource to understand strand orientation associated terminology
@Caffeinated-Code Caffeinated-Code added the enhancement New feature or request label Oct 19, 2023
@edmundmiller edmundmiller self-assigned this Oct 19, 2023
@edmundmiller edmundmiller added this to the v2.2.0 milestone Oct 19, 2023
@edmundmiller edmundmiller modified the milestones: v2.2.0, 2.3.0 Feb 14, 2024
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@edmundmiller edmundmiller

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enhancement New feature or request
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@edmundmiller @Caffeinated-Code