Basic transcriptomics: RNA-seq experiments and their analysis

Vincent J. Carey, stvjc at channing.harvard.edu

October 21, 2022

Upstream: dealing with FASTQ and sequencer QC

Alignments: BAM, Rsamtools, GenomicFiles

Midstream: handling counts, SummarizedExperiment

Quantification vs. alignment: Salmon, tximport

Downstream: Differential expression