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Month: December 2017

How to map long Oxford Nanopore reads to reference genome (and view in IGV)

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…

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