What You Get From RNA-Seq, and How to Analyze It
A file-by-file walkthrough of RNA-seq output: FASTQ, BAM, quant.sf, count matrices, and QC reports, plus the pipeline and the interpretation rules we would use on your own data.
Tag: qc
4 posts
How Many Reads You Need for RNA-Seq
A practical answer to RNA-seq depth: 30-40 million paired-end reads for whole-blood expression profiling, why the number moves with your question, and how to check that you got what you paid for.
How to Analyze Your Own Whole-Genome Sequencing Data
A working pipeline for taking 30x PCR-free FASTQs to aligned CRAM, a filtered and annotated variant set, structural variants, and the QC numbers that tell you whether any of it is trustworthy.
What to look for in a genome kit
A genome kit is worth buying only if it ships you 30x PCR-free whole-genome sequencing and the underlying files. Here is the spec sheet, the QC commands to run on delivery, and what drugstore DNA kits measure.