Last week's data wrangling produced eight FASTQ files containing the sequencing reads for my genome ($8=4 \times 2$, four lanes' worth of paired-end reads). The next step in making sense of these 1.3 billion reads is to map their positions of origin in the human reference genome assembly. This post will continue somewhat down in the weeds technically, but we'll end up in position to look at some interesting genetics next time.
If you're not interested in the technical minutiae - and that would be fair enough - you could skip to the last section.
Reads quality control with FastQC
Trust, but verify: since my data came from Illumina's CLIA lab, I wasn't terribly worried about gross quality problems - but some QC is always prudent before proceeding further. We have an app on DNAnexus to run reads through FastQC, which runs some essential sanity checks. I ran these on my four pairs of FASTQ files to get four FastQC reports. (It's worth examining the four lanes separately, because they could conceivably have independent quality issues.) Here's one representative plot: