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Category: bioinf

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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Get reads which map completely to reference using minimap (PacBio & Oxford Nanopore)

Get reads which map completely to reference using minimap (PacBio & Oxford Nanopore)

Minimap is a tool to find approximate mapping positions between two sets of long noisy reads or between genomes and long noisy reads like PacBio of Oxford Nanopore data (https://github.com/lh3/minimap). Standard output is in PAF format (https://github.com/lh3/miniasm/blob/master/PAF.md). If you want to filter the PAF file for reads which map entirely (or close to complete) to a genome you can use this simple awk command: awk ‘{if(($4-$3)>(0.9*$2)) print}’ mapping.paf > mapping.filtered.paf Nothing fancy at all. But it might help for example…

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