Tag: reference-genome

The public genome sites worth using, what each is good for, and how to go from a reference genome to a file that describes your own.

A practical guide to the three things people mean by genome mapping, the aligners and flags we would use on a personal whole-genome dataset, and what the compute costs.

hg19 is UCSC's packaging of the GRCh37 human reference assembly. They are nearly the same sequence with different chromosome names and a different mitochondrion, and the coordinates do not match GRCh38. Here is how to tell which build your files use and how to move between them without corrupting your data.

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.