Hi Jia, I would start by reading the help docs on chains and nets:
http://genome.ucsc.edu/goldenPath/help/chain.html http://genome.ucsc.edu/goldenPath/help/net.html Those explain chains and nets and how the files are constructed. I'm not totally sure what you are expecting to see but are not. For example, if I click on the net showing at the position you listed (chr7:25681793-25788913), it has an ID of 5. If I look in the rbest.net file, I find the line corresponding to that, here: fill 1730704 157395378 chr7 + 370509 158704532 id 5 score 11940049674 ali 135239485 qDup 1095596 type top If you are comfortable building some of our utilities from source (http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads), here are command lines that extract the rbest chain that overlaps that region and the complete structure of the enclosing rbest net: |chainFilter hg19.panTro3.rbest.chain.gz -t=chr7 -tOverlapStart=25681792 -tOverlapEnd=25788913> HOXA_region.chain| |netFilter hg19.panTro3.rbest.net.gz -t=chr7 -tOverlapStart=25681792 -tOverlapEnd=25788913> HOXA_region.net| chainFilter and netFilter both have many other options described in their usage messages. For understanding the positive and negative strand entries, you may find this previous mailing list answer helpful: https://lists.soe.ucsc.edu/pipermail/genome/2011-November/027526.html I hope that helps! Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 4/23/12 2:35 PM, Zeng, Jia wrote: > Hi, > > I'm trying to infer orthologous regions between two different species using > the chain and/or net file provided by UCSC. To understand how to do this, I > decided to use a > well conserved region (the HOXA cluster from human genome) as inquiry. This > region's coordinate (panning from HOXA1 to HOXA13) is chr7:25681793-25788913 > in hg19. > Due to HOX genes' high conservation level, I expect there to be a > corresponding region in the Chimp genome. > > To check whether this is indicated by the chain/net files, I downloaded the > hg19.panTro3.rbest.chain and hg19.panTro3.rbest.net files. For some reason, I > didn't locate > any chain/net that overlap with the aforementioned region although if I input > the said region on genome browser and turned on the comparative genomics > track. it seems > that the Chimp Alignment Net does exist for this region. > > I suspect that I may have some fundamental misunderstanding about the files > of interest and I also am not very clear about the practical difference > between the rbest.chain > and rbest.net files. Your input will be greatly appreciated. > > Best, > - Jia > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
