Good Afternoon Jia:
I tried this sequence of commands here to see if there is any change
in our programs. I obtain the identical results that we delivered in 2009.
I ran this csh script:
#!/bin/csh -efx
cd /tmp/synNet/axtChain
# filter net for synteny and create syntenic net mafs
netFilter -syn hg19.rheMac2.net.gz \
| netSplit stdin synNet
chainSplit chain hg19.rheMac2.all.chain.gz
cd /tmp/synNet
mkdir axtSynNet
foreach f (axtChain/synNet/*.net)
netToAxt $f axtChain/chain/$f:t:r.chain \
/scratch/data/hg19/hg19.2bit /scratch/data/rheMac2/rheMac2.2bit stdout \
| axtSort stdin stdout | gzip -c > axtSynNet/$f:t:r.hg19.rheMac2.synNet.axt.gz
end
Using the files you find on hgdownload:
-rw-rw-r-- 1 80508577 Nov 10 16:22 hg19.rheMac2.net.gz
-rw-rw-r-- 1 54624334 Nov 10 16:23 hg19.rheMac2.all.chain.gz
-rw-rw-r-- 1 816241703 Mar 8 2009 /scratch/data/hg19/hg19.2bit
-rw-rw-r-- 1 746913825 Jan 30 2006 /scratch/data/rheMac2/rheMac2.2bit
Resulting file is identical to the hgdownload version:
-rw-rw-r-- 1 4677891 Nov 10 16:47 chrY.hg19.rheMac2.synNet.axt.gz
Check your procedure script and source files to see if they match the
example here.
--Hiram
----- Original Message -----
From: "Jia Zeng" <[email protected]>
To: [email protected]
Sent: Thursday, November 10, 2011 3:22:40 PM
Subject: [Genome] About generating syntenic net alignments
Hi,
I need to obtain the syntenic net alignments between several mammalian genomes
and I decided to generate them myself.
Given the information provided in the script doBlastzChainNet.pl (in particular
the doSyntenicNet subroutine), I located the
following script:
# filter net for synteny and create syntenic net mafs
netFilter -syn $tDb.$qDb.net.gz \\
| netSplit stdin synNet
chainSplit chain $tDb.$qDb.all.chain.gz
cd ..
mkdir $successDir
foreach f (axtChain/synNet/*.net)
netToAxt \$f axtChain/chain/\$f:t:r.chain \\
$defVars{'SEQ1_DIR'} $defVars{'SEQ2_DIR'} stdout \\
| axtSort stdin stdout \\
| axtToMaf -tPrefix=$tDb. -qPrefix=$qDb. stdin \\
$defVars{SEQ1_LEN} $defVars{SEQ2_LEN} \\
stdout \\
| gzip -c > mafSynNet/\$f:t:r:r:r:r:r.maf.gz
end
rm -fr $runDir/synNet
rm -fr $runDir/chain
Since the $tDb.$qDb.net.gz, $tDb.$qDb.all.chain.gz files can be downloaded from
the goldenPath directory of the download
repository, I figured that I can easily complete the generation procedure
following the script provided. (I do not need to represent
the alignments in MAF form so I stopped at step netToAxt and wrote the output
axt to chr?.$tDb.$qDb.synNet.axt, following UCSC's
naming convention).
In order to ensure that I have successfully generated the synNet.axt files, I
downloaded the following file from UCSC website:
chrY.hg19.rheMac2.synNet.axt.gz and compared it with the one generated by me. A
diff indicated some differences in the two files
for instance, in UCSC's version, such an entry exists which is absent in my
file, though the entries before and after it are identical.
92 chrY 873749 873891 chr3 158314483 158314625 - 9481
It seems that my version has filtered out more entries than UCSC's version. I
am just wondering whether you could kindly offer an
input to this? Thank you very much.
Best,
- Jia
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