Closed mrshu closed 6 years ago
lastdb genome.fa genome.fa lastal genome.fa genome2.fa -E 1e-20 > firstSecond.maf' maf-convert psl firstSecond.maf > tmp.psl # keep only alignments of length at least 100 in both sequences perl -lane 'die unless @F==21; $s = $F[12]-$F[11]<100 || $F[16]-$F[15]<100; print unless $s' tmp.psl > tmp100.psl pslToChain tmp100.psl tmp100.chain # kent tools binary on genomika # fix bad coordinates on reverse strand perl -lane 'if ($F[0] eq "chain" && $F[9] eq "-") { ($F[10],$F[11]) = ($F[8]-$F[11], $F[8]-$F[10]); print join(" ", @F) } else { print }' tmp100.chain > firstSecond.chain