For stranded data, I use "bedtools genomecov" with -strand to generate coverage plots. For single reads, this works fine, but for paired-end reads, it doesn't actually take mate pairs into account. Thus, half the data (reverse reads) ends up on the "wrong" strand. Is there a way to generate coverage plots for paired-end stranded data?
Is the only solution to split the BAMs, process them separately, and then merge? That seems like a lot of work. Also, very heavy on the I/O.
Is the only solution to split the BAMs, process them separately, and then merge? That seems like a lot of work. Also, very heavy on the I/O.
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