(G) Chains between genomes (medium, needs A from both groups)

[mrshu]

• The goal is to create chains from malGlo to malSym and vice versa
  • Each group creates chains from its browser to the other browser
• This is done similarly as self-similarity chains, but alignments are done between two different genomes and filtering is done differently

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

• trackDb.ra record similar, but include target species in line with type chain