LiftOver Howto
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Revision as of 10:47, 29 June 2010 by Max (talk | contribs) (New page: 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 == * BL...)
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
- 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 bsub blat ../ci2.2bit $i -tileSize=12 -fastMap -minIdentity=98 psl/`basename $i .fa.masked`.psl -noHead -minScore=100; done
