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How do I find all supplementary mappings of a chimeric long (ONT) read mapped with NGMLR?

Bioinformatics Asked by Liam McIntyre on March 10, 2021

Unlike this guy How do I find split reads? I have done a lot of reading before asking this question. I’m aware that the FLAG will tell me if a read is supplementary and the CIGAR has information pertaining to soft clipping.

What I can’t figure out is how to get detailed information from one alignment about where its chimeric partners are, like what you get in IGV by inspecting the read details. Is there enough information in the cigar to identify multiple interchromosomal translocations, for example? Or do I need to parse the whole BAM and match up read names to get all the data the IGV displays?

Thanks!

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