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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.
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.
Strand Flipping: Deeptools Bamcoverage
Note: Nice resource to understand strand orientation associated terminology
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