Same species lift over construction: Difference between revisions
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and the comments in it to setup the workDirectory and your two genome sequences. That script also | and the comments in it to setup the workDirectory and your two genome sequences. That script also | ||
uses [[File:BlatJob.csh.txt]] | 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. | |||
Revision as of 05:45, 13 March 2013
Same Species Lift Over
Same species lift over procedure. There is a different procedure for different species lift over construction: Minimal_Steps_For_LiftOver
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.
