Hi Luvina, Thank you very much for the help. The chain file is very useful to my research. Inspired by it, I'm also interested in the rbest.chains of hg19 vs rheMac2 and panTro3 vs rheMac2.
I understand that you guys have a very busy schedule and I do not want to bother too much. Is it possible for you to outline the procedure to generate these files so I can do it by myself? Thank you once again. Best, - Jia ________________________________________ From: Luvina Guruvadoo [[email protected]] Sent: Tuesday, August 02, 2011 6:14 PM To: Zeng, Jia Cc: [email protected] Subject: Re: [Genome] Locating orthologous regions (not just genes) between human and chimp Hi Jia, The rbest.chain file for hg19 vs panTro3 is now available here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/reciprocalBest/ Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 6/28/2011 10:24 AM, Luvina Guruvadoo wrote: 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]<mailto:[email protected]> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected]<mailto:[email protected]> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
