Hi, Luvina: Thank you for your quick response. It turns out this tool is very helpful to my specific question.
I just have one more question. When the liftOver tool perform the coordinates conversion from human genome to the chimpanzee genome, dose it based upon the BLAT alignment, or any other resource? Thanks. Jia ----- Original Message ----- From: "Luvina Guruvadoo" <[email protected]> To: "Jia Zeng" <[email protected]> Cc: "genome" <[email protected]>, [email protected], "Soojin Yi" <[email protected]> Sent: Friday, May 6, 2011 2:43:50 PM Subject: Re: [Genome] Question about human and chimpanzee comparative analysis Hi Jia, The Batch Coordinate Conversion (liftOver) utility is a useful tool for converting coordinates between assemblies. From the main page, click on 'Utilities' located on the left-side menu, then click on 'Batch Coordinate Conversion (liftOver)'. Here, you can select your original genome/assembly (human/hg18) and new genome/assembly (chimpanzee), and upload your BED file. Once you have submitted your data, scroll down and click on 'View Conversions'. Your results will be displayed in BED format. For general information on how to use the liftOver utility, see: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert. Please feel free to search the Genome mailing list archives by visiting our home page and clicking on "Contact Us" (http://genome.ucsc.edu/contacts.html), or email us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Zeng, Jia wrote: > 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
