Microarray Analysis

Seq. Data





Sequencing Data Help

View Seq Data: UCSC Genome Browser

The GUDMAP Track Hub organises all sequencing samples into composite tracks, with each one represetning the sample from a given series. Each series can be viewed/browsed on the GUDMAP Sequencing Series page, with all individual samples available on the GUDMAP Sequencing Samples page.

All GUDMAP Sequencing Data Samples are accessible on the UCSC Genome Browser by using the GUDMAP Track Hub. Below are brief instructions for loading the GUDMAP Track Hub into your UCSC Genome Browser session, but UCSC provides more detailed help on using track hubs on it's website.

1. Go to UCSC Genome Browser Gateway and click on the 'track hubs' button.

UCSC Genome Browser gateway

From here select the 'My Hubs' tab and enter the following URL into the box: http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/hub.txt, then click 'Add Hub'.

Adding tasck hub in UCSC

Now when you view the genome, the GUDMAP tracks should be available, controls for display are found under the main browser panel in the track controls section. Please note, GUDMAP tracks are organised by series, with only the first track in each series visible by default. Performance is compromised when viewing a large number of tracks at once.

Display of GUDMAP track hub

2. You can load up the GUDMAP Data Track Hub directly by adding it's URL into your browserURL. "If you add hubUrl=[URL] to your hgTracks URL line, it will add the hub directly into the browser (e.g. http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&hubUrl=http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/hub.txt)."

To load up the track hub at a specific gene location use http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&hubUrl=http://www.gudmap.org/Gudmap/ngsData/gudmap_ucsc_hub/hub.txt&position=[gene symbol]

To select specific GUDMAP tracks and change their display find the track's controller in the Track Controls section at the bottom of the Genome Browser page, select the desired mode from the control's display menu, and then click the refresh button. To access filter and configuration options for a specific annotation track, open the tracks' description page by clicking the label for the track's control menu under the Track Controls section, the mini-button to the left of the displayed track, or the "Configure..." option from the Genome Browser's right-click popup menu. Please view the UCSC Guide to using the Genome Browser for complete help in viewing and displaying tracks.

View Seq Data: Integrative Genomics Viewer (IGV)

The following instructions should be used to run IGV and set-up the preferences to enable GUDMAP Sequencing Data Samples to be viewed. If you have any queries about setting it up please e-mail the GUDMAP Editoral Office.

1. Download/Run IGV from (http://www.broadinstitute.org/software/igv/download)

IGV Download

2. Once running go to View > Preferences and select the Advanced tab

Set the Genome Server URL to: http://igv.broadinstitute.org/genomes/genomes.txt

Set the Data Registry URL to: https://www.gudmap.org/Gudmap/ngsData/gudmap_registry2.txt

Click OK

Set server on IGV

3. Now select "Load from Server" from the File menu

4. Select sample to view from tree

Select sample on IGV - Load from Server

View Seq Data: Access from Gene-Strips

It is also possible to link directly to either UCSC or IGV from gene-strips on GUDMAP. The links are set-up to open on a view of each browser at the genomic location for that gene.
No sequencing samples are specified, so a default view of 1 or 2 samples from each series are displayed by default. Users can modify the settings from with UCSC or IGV to display samples of interest.