Same species lift over construction

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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.

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