liftOver over.chain file creation

[Thomas Darde]

Would it be possible to have an access to the same exact conversion pipeline to generate our own .over.chain files ?

In the past, we tried to create these files by following the information available from the links below (http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver
http://genomewiki.ucsc.edu/index.php/LiftOver_Howto). It seems that these wiki pages allow one to generate all.chain file but not the .over.chain file, so what is the difference between all.chain file and over.chain file

Do you have an other link that explain how to generate .over.chain file?
Do you have an other pipeline (perl, python, shell script) dedicated to the creation of the .over.chain files?

Thank you again for your precious help.

Best wishes,

Thomas DARDE
PhD student, FRM funding
GenOuest facilities / IRSET
==========================================
Inserm U1085 IRSET, 
Bureau 253, 9 Avenue du Professeur Léon Bernard
35000 Rennes - France 
==========================================
Web : thomasdarde.fr

[Hiram Clawson]

Good Morning Thomas:

Please note our script that we use to perform all steps of the procedure, at lines 937-944:

http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/utils/automation/doBlastzChainNet.pl

937 # Make nets ("noClass", i.e. without rmsk/class stats which are added later):
938 chainPreNet $inclHap $chain $defVars{SEQ1_LEN} $defVars{SEQ2_LEN} stdout \\
939 | chainNet $inclHap stdin -minSpace=1 $defVars{SEQ1_LEN} $defVars{SEQ2_LEN} stdout
/dev/null \\
940 | netSyntenic stdin noClass.net
941
942 # Make liftOver chains:
943 netChainSubset -verbose=0 noClass.net $chain stdout \\
944 | chainStitchId stdin stdout | gzip -c > $tDb.$qDb.over.chain.gz

When the variables are expanded into a script to perform this procedure on a specific
pair of genomes, it can look something like this:

# Make nets ("noClass", i.e. without rmsk/class stats which are added later):
chainPreNet panPan2.panTro4.all.chain.gz /hive/data/genomes/panPan2/chrom.sizes
/hive/data/genomes/panTro4/chrom.sizes stdout \
| chainNet stdin -minSpace=1 /hive/data/genomes/panPan2/chrom.sizes
/hive/data/genomes/panTro4/chrom.sizes stdout /dev/null \
| netSyntenic stdin noClass.net

# Make liftOver chains:
netChainSubset -verbose=0 noClass.net panPan2.panTro4.all.chain.gz stdout \
| chainStitchId stdin stdout | gzip -c > panPan2.panTro4.over.chain.gz


--Hiram

On 5/31/16 8:44 AM, Thomas Darde wrote:
> Would it be possible to have an access to the same exact conversion pipeline to generate our own .over.chain files ?

> In the past, we tried to create these files by following the information available from the links below (http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver <http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver>
> http://genomewiki.ucsc.edu/index.php/LiftOver_Howto <http://genomewiki.ucsc.edu/index.php/LiftOver_Howto>). It seems that these wiki pages allow one to generate all.chain file but not the .over.chain file, so what is the difference between all.chain file and over.chain file

[Hiram Clawson]

> Would it be possible to have an access to the same exact conversion pipeline to generate our own .over.chain files ?

> In the past, we tried to create these files by following the information available from the links below (http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver <http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver>

> http://genomewiki.ucsc.edu/index.php/LiftOver_Howto <http://genomewiki.ucsc.edu/index.php/LiftOver_Howto>). It seems that these wiki pages allow one to generate all.chain file but not the .over.chain file, so what is the difference between all.chain file and over.chain file