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tommyau / bamclipper

Remove primer sequence from BAM alignments by soft-clipping
MIT License
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Output metrics #8

Open OldManTae opened 6 years ago

OldManTae commented 6 years ago

Hi there,

I have found the tool very straight forward and useful to use! I just had a question regarding metric outputs - is there a way to output which pairs were clipped and how many times? Since the script already clips in pairs, having the metrics would prove very useful to assess pair based coverage

Thanks in advance!

tommyau commented 6 years ago

Thank you for your suggestion. I have some internal code that tags amplicon name to modified SAM alignment line, so that you can extract which (& how many) read pairs come from a given amplicon. Please see if that could be useful to you?

OldManTae commented 6 years ago

Hi Tommy,

Thank you for your reply! The code you mentioned would be very useful! Is this already in the program? I can give it a go see if it works well for the counting process (which sounds like it will)

Thanks again!