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

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.


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.