Hello Jia, Apologies for the delay in replying. One of our developers had this to say about your question:
In panTro2, both of those example regions match with Other RefSeq annotations. Chimp RefSeq is extremely sparse (<1500 genes), so it can't be used to determine "intergenic". Human refGene ought to be a pretty good proxy because of the high similarity between human and chimp. Ensembl and other gene prediction tracks might also be useful. Note that you may also find the pslMap tool handy as it is actually meant for lifting over items with finer structure like genes. You can find more information on pslMap in this previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2008-September/017126.html Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu > To whom it may concern: > > I would like to use UCSC genome browser to do some comparative analysis > between human and chimpanzee. Right now I have the genome coordinates for the > region of interest in human (hg18), and I would like to look for the > orthologous site in the chimpanzee genome. > > I have the coordinates in human as BED format, here is the part of the file: > > chr11 66346610 66346721 3 200 + > chr14 90693735 90693787 4 200 + > chr3 197937922 197938039 5 200 + > chr1 143729237 143729356 6 200 - > > I wonder if I can directly use this file as an input, and utilize some tool > in UCSC genome browser to directly get the coordinates of orthologous site in > the chimpanzee. It would be nice if the output file has the same format as my > input. > > Thank you so much and I am looking forward to your reply. > > Best, > > Jia Zeng > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
