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]] | ||
The 'sameSpeciesBlatSetup.sh' script partitions each genome sequence into single parts, expecting small genomes | |||
with chromosome sizes less than 10,000,000 bases each so that no chromosome is broken into separate | |||
parts. The two resulting parts lists are matched together so that each part from each genome is matched | |||
with every other part of the other genome. This generates a job-list shell script for each of those parings. | |||
The BlatJob.csh script runs the blat for each pair to generate PSL file results which are used in the chain/net step. | |||
=Step 2 - chain/net= | =Step 2 - chain/net= | ||
Revision as of 17:38, 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
The 'sameSpeciesBlatSetup.sh' script partitions each genome sequence into single parts, expecting small genomes with chromosome sizes less than 10,000,000 bases each so that no chromosome is broken into separate parts. The two resulting parts lists are matched together so that each part from each genome is matched with every other part of the other genome. This generates a job-list shell script for each of those parings. The BlatJob.csh script runs the blat for each pair to generate PSL file results which are used in the chain/net step.
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.
