*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]> 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 at > http://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]] 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]> 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> > >> > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > >
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