How to Trim RNA-seq Reads
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.
Tag: fastq
3 posts
How to Trim Sequencing Reads Without Distorting Your Own 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.
Getting Cell Ranger to Accept Your FASTQ Files
A working guide to the FASTQ layout, naming, and read structure Cell Ranger expects, how to produce those files from BCLs, how to verify them before you burn compute, and what to do when the pipeline says it found nothing.