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2.2 years ago
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I would like to annotate RNA-seq alignments with the strand on the genome they come from. I can do a brute force method using GTF file and for every read look up the strand information and store it as a tag. However I would like to do in a fast and efficient way.
The bitwise flag in the BAM file (2nd field) already has strand information. I guess I don't understand why you would need to look it up.
No the flag only tells you either forward or reverse complement of the 'read' is mapped to the genome. If I knew the directionality of the reads in the first place I could use that information. However my reads are split half half between strands of the input cDNA so regardless of gene strand half maps to positive strand and half to negative. However every gene has a true strand which I need to know.