I am trying to get data from a minION run I have done. Most of my reads a pretty low quality (rapid seq kit with shortened fragmentation on 8kb plasmid...might be the problem?) and over half failed. I've tried to use a few aligners like bwa-mem, graphmap, last - but nothing is aligning to my plasmid. Is it worth it to to try the failed reads? Will I get usable/ok data with enough coverage?
Is there a way to extract fastq/a files from just the failed reads using poretools or nanoOK? Any tips would be appreciated!