Hi Michiel, We specified M=50 for our lastz run without any other arguments, therefore it should have had the defaults of lastz which states L= K == 3000.
We may have a bug in our creation of the download README file where we state L=2200 as a default. We are going to look into it. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 10/30/11 8:08 AM, Michiel de Hoon wrote: > To answer my own question, the discrepancy appears to be due to a bug in > lastz that causes an incorrect value for L to be printed. I have informed the > lastz author of this problem. > > Thanks, > > -Michiel de Hoon > RIKEN Yokohama > > > > > > > > Dear UCSC, > > To make sure I understand the pairwise genome alignment process, I am trying > to regenerate the canFam2-equCab2 alignment. I am getting something close but > not quite the same as the alignment available from UCSC. > > One thing I was wondering about are the parameters used for the lastz runs. > According > toftp://hgdownload.cse.ucsc.edu/goldenPath/canFam2/vsEquCab2/README.txt, > K=3000 and L=2200 were used (in addition to O=400 E=30 H=2000 M=50). However, > the .net.axt.gz files have the following lines in their header: > > ##aligner=lastz.v1.00.05 H=2000 M=50 > ##blastzParms=O=400,E=30,K=3000,L=3000,M=0 > > suggesting that L=3000 was used instead of L=2200 (I also assume that M=50 > was used instead of M=0, since we don't remove repeat regions from these > genomes before aligning). > > Which are the correct lastz parameters to use? > > Many thanks, > > Michiel de Hoon > RIKEN Omics Science Center, Yokohama > > > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
