3 posts
A practical guide to moving variants, intervals, and gene models between GRCh37, GRCh38, and T2T-CHM13 using chain-based liftover, Liftoff, and LiftOn, with checks that tell you when the result is wrong.
A working guide to lifting positions, VCFs, intervals, and probe manifests between GRCh37, GRCh38, and T2T-CHM13, including which tool to use for each file type and how to tell when the lift silently went wrong.
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.