Tag: fastq

A step-by-step method for deciding whether a failing FastQC module means your library is broken, your sequencer had a bad run, or the plot is simply behaving as designed.

A practical walkthrough of working with raw sequencing reads: reading the format, checking quality, aligning to a reference, and knowing when the data is good enough to call variants.

A working guide to the files a sequencer produces and what to do with them: FASTQ through alignment, variant calling, annotation, and RNA quantification, with the commands, parameters, and failure modes that matter.

A practical guide to adapter, quality, poly-G and poly-A trimming for RNA-seq FASTQs: which tools to use, the exact flags, how much trimming is enough, and how to verify you did not damage the data.

A practical trimming workflow for personal whole-genome and RNA-seq FASTQs: how to find the real adapter, which tool and flags we use, how gently to trim, and how to verify that trimming helped rather than shifted your expression estimates.

The FASTQ layout, naming and read structure Cell Ranger expects. Covers producing the files from BCLs, verifying them and a run that finds nothing.