Restrictive alignment with minimap2
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9 weeks ago
njornet ▴ 20

I need to align nanopore reads from human to a custom reference genome and I want to align only the reads that have a very high identity. I tried changing the missmatch penalty but if I increase it too much minimap raises a Segmentation fault error. Should I change something else in the configuration of minimap2 or should I filter the aligned reads by score or something and how would I do that?

Thank you!

nanopore alignment minimap2 • 293 views
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I want to align only the reads that have a very high identity

Filtering after the fact based on MAPQ or CIGAR's an option?

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If I have the resulting SAM it is right?

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