Building an RNA-seq Variant Calling Pipeline
A working GATK pipeline for calling SNPs and indels from RNA-seq reads, with filters suited to transcriptomic data and a check against genome calls.
Tag: star
3 posts
How to Align and Quantify Your Own RNA-seq Data
A working guide to turning personal RNA sequencing FASTQs into gene- and transcript-level expression estimates: reference choice, selective alignment with Salmon, spliced alignment with STAR, QC thresholds, and the checks that catch a swapped or degraded sample.
How to Choose and Build a Reference Genome for RNA-seq
A practical guide to picking a human genome build and annotation for RNA-seq, building STAR and salmon indexes correctly, and checking that the reference you built is the one your quantification assumes.