I am confused about the difference between
GRCh37.p13.genome.fa (767 MB, http://www.gencodegenes.org/releases/19.html) and
GRCh37.primary_assembly.genome.fa (830 MB http://www.gencodegenes.org/releases/27lift37.html) which is lifted from Gencode release 27. I want to use the most recent version of GRCh37, with the most corrections/updates/etc. I can't use GRCh38 because of alt loci making accurate quantification difficult.
I can see pluses and minuses for each choice. which genome should I be using for STAR genome alignments?
Perhaps there is a version of
GRCh37.p13.genome.fa which is lifted or related to release 27?