v34 (1 of 2): Genomes of human (hg38), and Guinea pig (cavPor3)

We've added reference genomes of human hg38 and guinea pig cavPor3 to the browser. All genome data including track files were downloaded from UCSC Genome Browser. We acknowledge the NCBI Genome Reference Consortium and UCSC Genome Browser team for their enormous efforts in generating these resources.

Human hg38 genome is listed as a minor item along the quite ancient hg18, since hg38 currently has no experimental assay tracks, and all of that is in hg19.

Go to http://epigenomegateway.wustl.edu/browser/ and click hg38 button to launch the new genome:

To find the guinea pig genome, click the "Rodentia" tab under "Animalia":

v33 (2 of 2): hide "undesirable items" from a track!

IF YOU REALLY WANT TO DO THIS, here's how:

Click the "gear" button to the right of the Apps button:

Check the checkbox labeled "Allow pack and hide", and read the message that appears underneath:

By keeping this checkbox checked, you have access to the "Pack and Hide" functions. Both functions allow you to alter a gene track by hiding "undesirable items". "Pack" can be used to remove items with identical names and overlapping coordinates.

E.g. there are multiple gene models for the human PAX5 gene, right click on the track and click the "PACK" button:

Only 1 PAX5 gene transcript will be left after "packing":

To delete the microRNA gene in the middle, click on it and push the "HIDE" button:

Then it's gone:

To make items reappear, zoom the browser by either zoom in or zoom out. YOU ONLY MODIFY THE RUN-TIME DATA in your web browser, but not the actual data on our server.


Disclaimer: By using this function you agree that you (but not us) will be responsible for any consequences of your actions.

v33 (1 of 2): upload long-range interaction data

From version 33 you can now upload long-range interaction data in the form of text files. This is very suitable for showing small quantity of data (including but not restricted to 5C, ChIA-PET, Hi-C results), and you don't need to go through trouble of converting your data into the required format and host it as a custom track.

To start, convert your data into a simple format like this:

chr1,713605,715737     chr1,720589,722848 2
chr1,717172,720090 chr1:761197-762811 2
chr1,755977,758438 chr1:758539-760203 2

Each line indicates an interaction event involving two regions from the genome. 3 fields are present for each line: coordinate of region 1, coordinate of region 2, score.

• For the coordinates, you can use a non-word character to separate fields, but don't use tab.
• The score is optional.
• Unlike that is required for the long-range interaction track format, do not make duplicating records for each of the interacting pairs.

Go to Apps > File upload:

Upload your file. At the "Edit" panel, choose "Pairwise interaction" option and click "Add" button. The track will be loaded: