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2.8 years ago
Hi, I'm trying to demultiplex nanopore sequencing reads based on barcodes using minimap2 I find that when generating a sam file, the alignments have a TLEN of zero, does this mean there was no alignment? I can generate PAF files but only "secondary" alignments are given, no "primary" alignments. I will write a custom script to filter these to the best match based on number of matching bases but if there was a way to generate a PAF file containing only the best match that would be ideal. Any help welcome. Thanks, Matt
Not answering your question but see if this helps: https://www.protocols.io/view/demultiplexing-nanopore-reads-with-last-7vmhn46
You should use
guppyto do the demultiplexing if possible.