Mate pair positions using pysam
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Entering edit mode
5.7 years ago

I can do this for the read in pysam

pos = read.positions

# returns a list of positions

I want to do this for the mate. There is no .mpositions but there is a .mpos

Thanks!

pysam mate pair python • 2.0k views
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5.1 years ago

hello, it seems that .mpos is deprecated by .next_reference_start now, but I still have a problem using it. if the mate read of a read exists and it is aligned to a position of the chrom, .next_reference_start returns a region of aligned mate reads or just the start?

Thanks a lot, Fredsamhaak

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Please make a new question horticulturesh, you've "answered" a few other questions with your own questions, which is not how this is supposed to work :P Write a new question, give as much code/data as you can, and you will get an answer :)