LiftOver Howto: Difference between revisions
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(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...) |
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* Sort/Chain/net | * Sort/Chain/net | ||
== Alignment == | |||
* I have repeatmasked my new genome assembly | * I have repeatmasked my new genome assembly | ||
* The masked fa files are in ../ci3/rm/masked | * The masked fa files are in ../ci3/rm/masked | ||
* I want the alignment .psl to be in the directory psl | * 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 | 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 | ||
Revision as of 10:47, 29 June 2010
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 bsub blat ../ci2.2bit $i -tileSize=12 -fastMap -minIdentity=98 psl/`basename $i .fa.masked`.psl -noHead -minScore=100; done
