Minimal Steps For LiftOVer

The following outlines the minimal steps I undertook to make a liftOver chain file to convert annotations between bacterial genome builds (genome size ~4Mb).

[1] Split the query (NEW) genome build by FASTA record using faSplit:

$ faSplit sequence NEW.build 2 chr

In this case, there are 2 fasta records in the build. Therefore, I used the argument '2' to split the build into two files which each contain one FASTA record.

[2] BLAT query sequences from [1] against the OLD build:

$ blat path_to_OLD_build/OLD.2bit path_to_NEW_build/chr0.fa OLD.chr0.psl -tileSize=12 -minScore=100 -minIdentity=98 -fastMap

$ blat path_to_OLD_build/OLD.2bit path_to_NEW_build/chr1.fa OLD.chr1.psl -tileSize=12 -minScore=100 -minIdentity=98 -fastMap