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Mate pair positions using pysam

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!

python pysam mate-pair
• 3,115 views • link
updated by Ram Ram • written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

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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updated by Ram Ram • written by horticulturesh • horticulturesh

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 :)

• 0 views • link
written by John John

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