# 3/7/2022 - Lou
cd /hive/data/genomes/mm39/bed/ncbiRefSeq.2020-10-27
#From following link: https://www.ncbi.nlm.nih.gov/nuccore/?term=mouse%5Borgn%5D+refseq_select%5Bfilter%5D
#Send to -> Complete record -> File -> Format: Accession list
#Saved as mm39RefSeqSelect.seq
zcat /hive/data/genomes/mm39/bed/ncbiRefSeq.2020-10-27/process/mm39.curated.gp.gz | fgrep -f mm39RefSeqSelect.seq > refseqSelect.curated.gp
wc -l refseqSelect.curated.gp
20584 refseqSelect.curated.gp
hgLoadGenePred -genePredExt mm39 ncbiRefSeqSelect refseqSelect.curated.gp

# trackDb entry added to mouse/trackDb.ra for both mm10+mm39, and html copied from hg19 (no mention of MANE)
track ncbiRefSeqSelect
parent refSeqComposite off
priority 8
type genePred
shortLabel RefSeq Select
longLabel NCBI RefSeq Select: One representative transcript per protein-coding gene
trackHandler ncbiRefSeq
idXref ncbiRefSeqLink mrnaAcc name
color 20,20,160
baseColorUseCds given
baseColorDefault genomicCodons