*Thanks a lot. I'll try different links for those data.
Best regards. Sincerely, Ben * On Fri, Jul 6, 2012 at 5:41 PM, Luvina Guruvadoo <[email protected]>wrote: > Hi Ben, > > In order to view the tracks, you will need to set Data Format to "Any" on > the Track Search page. The BAM files you are referring to can be downloaded > from the link my colleague provided below: > http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeHaibTfbs. You > can also access the downloads page by clicking "Downloads" from the track > description page for whichever track you are interested in. > > > Please contact us again at [email protected] if you have any further > questions. > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > On 7/5/2012 4:01 PM, FindMyRoom wrote: > > *Hello Steve, > > Following the steps in your last mail, I can't find such **HudsonAlpha TF > Binding Sites track you > provided,*http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs > *see the attached snapshot. > > Because I want to download the aligned file (BAM format), the link > *http://genome.ucsc.edu/cgi-bin/hgGateway* can only display wiggle files for > visualization. > > Could you please suggest how to redirect to the "**HudsonAlpha TF Binding > Sites track" in first link? > > The 2nd question, I want to download DNase-seq data (aligned BAM format), > while in HG19 and HG18, there are only wiggle files. Could you please > provide links for the aligned BAM-formatted data? > ** > Many thanks for help. Thanks. > > Sincerely, > Ben > * > > On Wed, Jun 20, 2012 at 2:05 PM, Steve Heitner <[email protected]> > <[email protected]> wrote: > > > Hello. > > The track that contains the data you are interested in is the ENCODE > HudsonAlpha Transcription Factor Binding Sites track > (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs). > You > can find the list of downloadable files > athttp://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeHaibTfbs. To > list > only the T-47D files, click the "Cell Line" box, check the "T-47D" checkbox > and then click the "close" button at the bottom of that menu. Click any > "Download" button in the leftmost column to download the corresponding > file. > > In the future, you can locate tracks of interest to you by using our track > search feature. The following is an example of how to locate T-47D > ChIP-seq > tracks: > > 1. Go to http://genome.ucsc.edu/cgi-bin/hgGateway > > 2. Click the "track search" button just under the clade/genome/assembly > drop-down lists > > 3. Click the "Advanced" tab > > 4. On the "Cell, tissue or DNA sample" line, click the text box and check > the "T-47D" checkbox > > 5. On the "Antibody or target protein" line, click the drop-down box and > change "Antibody or target protein" to "Experiment (Assay) type" > > 6. Click the text box on that same line and check the "ChIP-seq" checkbox > > 7. Click the "search" button > > Any tracks containing the information you specified will be listed in the > search results. To view those tracks, simply click the checkbox to the > left > of the corresponding result and then click the "View in Browser" button. > > Please contact us again at [email protected] if you have any further > questions. > > --- > Steve Heitner > UCSC Genome Bioinformatics Group > > -----Original Message----- > From: [email protected] [mailto:[email protected] > <[email protected]>] On > Behalf Of FindMyRoom > Sent: Tuesday, June 19, 2012 3:52 PM > To: Greg Roe > Cc: [email protected] > Subject: Re: [Genome] For T47D histone modification data: > > *Hi Greg > > Would you please send me the links for BED or fastq format for these cell > lines? > > Many thanks. > > > * > On Tue, Jun 19, 2012 at 5:42 PM, Greg Roe <[email protected]> > <[email protected]> wrote: > > > Hi, > > We do have Chip-Seq data for this cell line, but unfortunately, not > Histone modifications. Sorry. > > If you have any additional questions, please reply to:[email protected] > - > Greg Roe > UCSC Genome Bioinformatics Group > > > On 6/18/12 12:47 PM, FindMyRoom wrote: > > > *Hello everyone, > > > I am searching for T47D histone modification ChIP-seq data, do you > have any link or data source? > > Many thanks. > > > * > ______________________________**_________________ > Genome maillist - > [email protected]https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.so > e.ucsc.edu/mailman/listinfo/genome> > <https://lists.soe.ucsc.edu/mailman/listinfo/genome> > > _______________________________________________ > Genome maillist - > [email protected]https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > _______________________________________________ > Genome maillist - > [email protected]https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
