Yes, we break up the equCab2 chrUn into its scaffolds. We did not break up the chrUn on canFam2. You can view our procedure in the source tree file canFam2.txt:
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/doc/canFam2.txt Note the equCab2 lastz run starting at line 2702 in this file. Note also the instructions for equCab2: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/doc/equCab2.txt --Hiram Michiel de Hoon wrote: > Dear UCSC, > > I am trying to create a multiple genome alignment of several organisms using > the UCSC tools. To make sure I understand the process correctly, I am trying > to recreate the alignment between canFam2 (target) and equCab2 (query). With > your kind help, the alignment I am getting is consistent with the alignment > on the UCSC website, except for alignments of any canFam2 chromosome to > equCab2 chrUn. > > I understand that chrUn consists of several contigs, which are concatenated > into one virtual chromosome separated by long stretches of N's. In my lastz > runs, I partitioned the chrUn chromosome into sections of 20,000,000 > nucleotides (and the canFam2 chromosome into sections of 10,010,000 > nucleotides with 10,000 nucleotides overlap). By comparing the UCSC > alignments to my alignments, it seems that there is some difference in how > the chrUn chromosome is partitioned. > > So my question is: How are the chrUn partitioned for the lastz runs? Is > equCab2 chrUn perhaps partitioned into its contigs? If so, is the canFam2 > chrUn then also partitioned into its contigs? And if both the equCab2 chrUn > and the canFam2 chrUn are partitioned into their contigs, doesn't the number > of lastz runs explode? > > Best wishes, and thank you in advance, > -Michiel de Hoon > RIKEN Omics Science Center, Yokohama _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
