these are the command line arguments to create a local blast database from the new genome assembly (in our case T. confusum), and then blast the large exon file to create what we will call a look up table.

retro-blast.commands

# to construct database from an assembly in the file
# conf.scaf.fa run this in the terminal
# it will create a blast database call confscaf

makeblastdb -in conf.scaf.fa -dbtype nucl -out confscaf

# next we want to blast our large exons against this db
blastn -query=/outputs/300+bpExons.fa -db=/blastDB/confscaf -outfmt='6 qseqid qstart sseqid sstart qlen length pident' -max_target_seqs=2 -out=info

# this produces the lookup table that we can then use to analyze the degree of synteny conservation