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Hi
I wanted to know how I can get the unmapped pair reads of mapped pairs (which in the BAM are located right next to their mapped pair, with the same alignment coordinate) with the pileup() function. I have tried the following parameters:
Hi
I wanted to know how I can get the unmapped pair reads of mapped pairs (which in the BAM are located right next to their mapped pair, with the same alignment coordinate) with the pileup() function. I have tried the following parameters:
AligmentFile.pileup(reference=seq_name, start=start, end=stop, fastafile=ref_genome, min_base_quality=0, min_mapping_quality=0, max_depth=100000, stepper='nofilter', ignore_overlaps=False, ignore_orphans=False)
But still to no avail. I know the fetch() function can do this, but I need to do it with the pileup function. Thank you!
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