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
