Lastz tuning procedure

To fetch proteins, assuming you have the kent userApps and $HOME/.hg.conf set to:

db.host=genome-mysql.cse.ucsc.edu
db.user=genomep
db.password=password
central.db=hgcentral

For example on hg38:

hgsql -N -e 'select * from genscan;' hg38 | cut -f2- > hg38.genscan.tab
rsync -a -P rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit ./

getRnaPred -peptides -genomeSeqs=hg38.2bit hg38 hg38.genscan.tab all hg38.genscan.pep

The blat command is:

blat -prot -oneOff=1 ${target}.genscan.pep ${query}.genscan.pep -out=maf ${target}.${query}.oneOff.maf