notes_for_coverage_assessment.txt

no combine
no trim
dump ref in ref.gen
make yml file using nano
use ost with bam files
primaery mappings to n=6
flagstats (already in use, use with samtools mean coverage/percent covered)
should get mean covarge and percent covered (using script?)
could do ratio between sub-genomes
sub genomes
small chromosomes ignore
run scafs 1-6 for n=6
run scafs 1-7 for n=7

only running setup, 3, and 4 for pipe
dont use unpaired reads
dar_1
NEN_1