Hello, Would you be able to add a bit more detail about your query path and desired results (comparison). It will help us to understand your question better and provide the best advice:
1) Exact track name and database of original dataset 2) Exact file and parameters you used to convert with liftOver to hg18 , and if the line command or web version was used. 3) Exact track name and database that you wish to compare to The Table browser would be a recommended tool to do the comparison, but both data sets need to be based on the same genomic. In general terms, one would be a custom track and the other a regular, native track and then the Table browser would be used to perform an intersection. If at all possible, datasets that include SNP data should be native and not lifted. Table browser help: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser Custom track help: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Hopefully we will be able to design a successful intersection with the additional information, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Indrani Datta" <[email protected]> wrote: > From: "Indrani Datta" <[email protected]> > To: "[email protected]" <[email protected]> > Sent: Friday, September 4, 2009 10:45:56 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] help > > Hello, > > I have downloaded pictar4 microRNA target dataset from UCSC table > browser and I am trying to convert > the position (Chr + position) to hg18 . I did used the Liftover > utility for this conversion. > But it only returned some of the converted annotation ( chr + > position). > > I wanted to know how can I link back to SNP in hg17 pictar data with > this converted hg18 position > information. I would really appreciate any information related to > this. > > Thanks, > Indrani > > ============================================================================== > CONFIDENTIALITY NOTICE: This email contains information from the > sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or > otherwise protected from disclosure. This email is intended for use > only by the person or entity to whom it is addressed. If you are not > the intended recipient, any use, disclosure, copying, distribution, > printing, or any action taken in reliance on the contents of this > email, is strictly prohibited. If you received this email in error, > please contact the sending party by reply email, delete the email from > your computer system and shred any paper copies. > > Note to Patients: There are a number of risks you should consider > before using e-mail to communicate with us. See our Privacy Policy and > Henry Ford My Health at www.henryford.com for more detailed > information. If you do not believe that our policy gives you the > privacy and security protection you need, do not send e-mail or > Internet communications to us. > > ============================================================================== > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
