Same species lift over construction: Difference between revisions
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Same species lift over procedure. There is a different procedure for different species lift over construction: [[Whole_genome_alignment_howto]] | Same species lift over procedure. There is a different procedure for different species lift over construction: [[Whole_genome_alignment_howto]] | ||
See also: [[Minimal_Steps_For_LiftOver]] | See also: [[Minimal_Steps_For_LiftOver]] | ||
== Prerequisites == | |||
These procedures are unix command line shell scripted operations. Users should be familiar with unix command | |||
line shell programming and have the kent source tree available to build the necessary kent programs. | |||
=Step 1 - blat= | =Step 1 - blat= | ||
Revision as of 17:32, 13 March 2013
Same Species Lift Over
Same species lift over procedure. There is a different procedure for different species lift over construction: Whole_genome_alignment_howto See also: Minimal_Steps_For_LiftOver
Prerequisites
These procedures are unix command line shell scripted operations. Users should be familiar with unix command line shell programming and have the kent source tree available to build the necessary kent programs.
Step 1 - blat
Decide on a workDirectory where all this is to be performed. Note the script: File:SameSpeciesBlatSetup.sh.txt and the comments in it to setup the workDirectory and your two genome sequences. That script also uses File:BlatJob.csh.txt
Step 2 - chain/net
The second step is encapsulated in the script: File:SameSpeciesChainNet.sh.txt Similar setup as for Step 1, working in the run.chain directory, constructs the result file. Read the script for information on how to use it and where the result is.
