Hi Adam, sorry for the delay, I thought that this was a lot more complicated that it actually is in the end...
your chipSeq dataset of interest www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM317591 indeed includes UCSC wiggle and bed tracks directly in the GEO data entry. The files are compressed as .gz files so the browser can open them directly. in theory you can just copy-paste the address of the corresponding bed file into the genome browser's custom track page. Unfortunately, the custom track loader cannot recognize them as compressed files as the URL does not end with bed.gz. Therefore I recommend this little workaround: In NCBi GEO: Choose the .bed.gz file of the sample you want, rightclick on the (http) link and copy it to the clipboard. Paste it into a word document, like this: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?mode=raw&acc=GSM317591&db=GSM317591_CD133%2DPolII%2Dsummary%2Dvstep.txt.gz&is_ftp=true Move the is_ftp=true parameter somehwere into the middle of the URL, just after the & sign, and add a &-sign afterwards as a separator, like this: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?mode=raw&acc=GSM317591&is_ftp=true&db=GSM317591_CD133%2DPolII%2Dsummary%2Dvstep.txt.gz Paste this link into the Custom track page of the genome browser at http://genome.ucsc.edu/cgi-bin/hgCustom, it will then appear as a "User supplied track" Hope this helps and if there are any problems don't hesitate to send email to the mailing list again. cheers Max On Fri, Jun 18, 2010 at 11:16 PM, Maximilian Haussler <[email protected] > wrote: > Hi Adam, > > Some GEO datasets include .zip or .tar.gz files in GEO that our > students open with programs like WinRAR. They've come across some > datasets that include files with the extension .bed in the archives. > These files can be directly loaded into the genome browser. You only > have to find out the right genome assembly but this is often either > noted in the paper or coded into the filename (e.g. "peaks.mm8.bed") > > However, most datasets just consist of raw array intensities. If you > know more about the various steps and tools to create a plot from > intensities on the genome browser, I'd be interested as well... > > cheers > Max > > > > > On Fri, Jun 18, 2010 at 11:09 PM, Mary Goldman <[email protected]> wrote: > > Hi Adam, > > > > We would like to apologize for replying to your question so late, but > > the email just arrived in our inbox today. We are sorry for any > > inconvenience this may have caused you. > > > > GEO's FAQ page is a good place to start understanding how to retrieve a > > variety of data formats from their website > > (http://www.ncbi.nlm.nih.gov/geo/info/faq.html). In order to view their > > data in the UCSC Genome Browser, it will need to be in one of our > > supported formats, listed here: > > http://genome.ucsc.edu/FAQ/FAQformat.html. Basic information about > > creating a custom track can be found here: > > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks. > > > > If you have any questions about GEO or their data please email them at > > geo at ncbi.nlm.nih.gov or search their website > > (http://www.ncbi.nlm.nih.gov/geo/). I hope this information is helpful. > > Please feel free to contact the mail list again if you require further > > assistance. > > > > Best, > > Mary > > ------------------ > > Mary Goldman > > UCSC Bioinformatics Group > > > > On 6/12/10 5:06 PM, Adam Goldfarb wrote: > >> I am new to the world of bioinformatics but am really interested in > >> using the UCSC genome browser to study ChIP-seq data deposited in > >> GEO. Is there a simple guide, i.e. "ChIP-seq custom track viewing > >> for idiots" that could help me get started--paper or website or > >> tutorial? > >> > >> Thanks much > >> > >> Adam > >> > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
