LiftOver Howto

Creating a liftOver file is very similar to a whole-genome alignment. Please see the page Whole_genome_alignment_howto for some background on tools and terminology.

Outline

• BLAT the new genome onto the old genome
• Sort/Chain/net

Alignment

• I have repeatmasked my new genome assembly
• The masked fa files are in ../ci3/rm/masked
• I want the alignment .psl to be in the directory psl

 for i in ../ci3/rm/masked/*.masked; do blat ../ci2.2bit $i -tileSize=12 -fastMap -minIdentity=98 psl/`basename $i .fa.masked`.psl -noHead -minScore=100; done