Question: filtering of mapped Nanopore reads
0
gravatar for m.eitel
4 weeks ago by
m.eitel0
m.eitel0 wrote:

Hi.

I am trying to filter a bam file. I mapped raw nanopore reads to a reference assembly and want to keep only reads that map (almost) full length. bwa mem and minimap2 softmask bases at both ends that do not match to the reference and I want to keep only those reads that map full-length and allowing for 40bp unmatched/softmasked bp on both ends. Tried Samclip, but it does not work (outputting text file instead of true sam file). Any ideas on how to filter otherwise?

Thanks Michael

ADD COMMENTlink written 4 weeks ago by m.eitel0

please, post a SAM example with a few reads + header on gist.github.com

ADD REPLYlink written 4 weeks ago by Pierre Lindenbaum111k
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