The binaries you are using are much too old. They are from years 2006 and 2007. I'm certain we have fixed a few bugs since then. Try using up to date source code with new binaries. Note the build instructions:
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source --Hiram ----- Original Message ----- From: "Jia Zeng" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Friday, November 11, 2011 11:33:34 AM Subject: RE: [Genome] About generating syntenic net alignments Hi Hiram, Thank you for your prompt reply. I noticed that I neglected to do the axtSort step in my previous attempt and I redid it with the complete sequence. Now the diff output between my version and UCSC version is a lot smaller than before but I'm still seeing differences. Take chrY for example, the first difference occurred in the following entry: UCSC: 6014 chrY 28725727 28727469 chr17 1974742 1976484 + 133306 Mine: 6014 chrY 28725727 28728984 chr17 1974742 1977914 + 241557 Just to be sure that we are using the same version of the data/programs, I list the exact places where I got them as follows: hg19.2bit: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ rheMac2.2bit: http://hgdownload.cse.ucsc.edu/gbdb/rheMac2/ hg19.rheMac2.net.gz: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsRheMac2/ hg19.rheMac2.all.chain.gz: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsRheMac2/ Also, I'm using the executable compiled by Jim Kent and distributed through his webpage: http://hgwdev.cse.ucsc.edu/~kent/exe/linux/ As well, I wrote up the following bash script to complete my procedures automatically: #!/bin/bash tDb=hg19 qDb=rheMac2 baseDir=~/bcm/data/genomes/$tDb.$qDb synNetDir=$baseDir/synNet chainDir=$baseDir/chain axtDir=$baseDir/axt tNibDir=~/bcm/data/genomes/$tDb/$tDb.2bit qNibDir=~/bcm/data/genomes/$qDb/$qDb.2bit if [ -e $synNetDir ] then echo "$synNetDir already exists" else netFilter -syn $baseDir/$tDb.$qDb.net.gz | netSplit stdin $synNetDir fi if [ -e $chainDir ] then echo "$chainDir already exists" else chainSplit $chainDir $baseDir/$tDb.$qDb.all.chain.gz fi cd $synNetDir if [ -e $axtDir ] then echo "$axtDir already exists" else mkdir $axtDir fi for f in *.net do echo $f if [[ $f =~ .+hap.+ ]] then echo "haplotype ignored (pseudochromosomes)" else inChain=$chainDir/${f/".net"/".chain"} outAxt=$axtDir/${f/".net"/".$tDb.$qDb.synNet.axt"} if [ -e $outAxt ] then echo "$outAxt already exists" else netToAxt $f $inChain $tNibDir $qNibDir stdout | axtSort stdin $outAxt fi fi done Thank you very much for your time in advance. Best, - Jia _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
