Psst! I've posted some details about my notebook setup here.

Loading paired reads from position-sorted BAM files

Permalink: 2018-06-12 by Daniel S. Standage in blog tags: ngs bam

BAM files with sequence alignments sorted by genomic position seem to be the new currency of exchange for large-scale human genome sequencing projects. This is convenient and practical in many ways for many people. But in my current research I work a lot with tools that only want/need the sequence information and, for whatever reasons, support only FASTA or ...

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How to distinguish perfectly mapped reads from a SAM/BAM file

In which I explore read alignments in SAM format and discuss the pros and cons of various approaches to distinguishing perfect matches from imperfect matches.

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An idiot's guide to loading reads from a BAM file

tl;dr? It's fine, just ignore secondary/supplementary alignments and don't disable reporting of unaligned reads.

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