3 posts
Read depth in RNA-seq is the number of reads assigned to your sample and, per gene, the number of reads supporting each transcript. This page explains how to compute it from your own files, why 30x means nothing here, and what depth to ask for.
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.
A practical guide to computing principal components from RNA-seq counts in R: which transform to use, how many genes to feed in, how to figure out what each component means, and when PCA is the wrong tool.