Hi Jia, We have noted your request and will notify you once the rbest.chain file for hg19 vs panTro3 has been released.
Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Zeng, Jia wrote: > Hi, > > I have this question and after searching the mailing-list archive, I found a > similar thread for which a UCSC staff member Jennifer gave a very good answer > to: (https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021123.html) > > But my question is a bit more general than the original post so I would > appreciate a bit more information. > > I need to perform a genome-wide search to locate all the orthologous regions > (including both non-coding and coding regions) in the human genome that are > orthologous to the chimp genome. From the original answer in the related > post, I have an impression that to do so, the best way is to get a hold of > the "best reciprocal alignment" between the human and chimp genome instead of > just the single directional alignment such as the files shown in > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/axtNet/ (I kind > of presume the single directional alignment does not necessarily imply > orthology since some regions in the human chromosome 1 correspond to the > chimp chromosome 15, which doesn't make sense). > > However I failed to locate the rbest.chain file in the newest human/chimp > assemblies, which used to exist in earlier assembly (eg. hg17 vs panTro1). > Could you please let me know how I can construct the best reciprocal > alignment between human and chimp using two single directional alignments > (human vs chimp and chimp vs human)? Can I just naively intersect the two > single directional alignments and retain the entries that exist in both > files? Please kindly advise. Thank you very much for your time in advance. > > 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
