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