How to map long Oxford Nanopore reads to reference genome (and view in IGV)
Very long Oxford Nanopore reads cause a problem with BAM format. The max. CIGAR operations permitted to store per read are 65535 (https://samtools.github.io/hts-specs/SAMv1.pdf). So if you want to convert SAM to BAM you get an error. However, using the newer CRAM format (https://samtools.github.io/hts-specs/CRAMv3.pdf) you can avoid this problem. Also, CRAM has a smaller memory footprint. Here, I am going to show you how to map ONP reads using Graphmap (https://github.com/isovic/graphmap) and converting to CRAM (using samtools) and then how to…