Prepare custom track of annotation data (or "bed" track)

0	Make sure you have the tabix program installed. You can download the latest source and compile: http://sourceforge.net/projects/samtools/files/tabix/ Or if you're using Ubuntu operating system, install it using apt-get: $ apt-get install tabix You should have both tabix and bgzip programs available on your computer.
1	Skip this step if your file is BED format. Run the command bigBedToBed in UCSC genome browser tool set and convert the bigBed file to a bed text file.
2	Compress the BED file: $ bgzip input.bed The old file is gone and a new file "input.bed.gz" is there instead.
3	Build tabix index of the compressed BED file: $ tabix -p bed input.bed.gz The "input.bed.gz" is untouched but an index file "input.bed.gz.tbi" is generated.
4	Display this file as a custom bed track on WashU Genome Browser. Put the .gz and .gz.tbi files on the SAME directory on your web server. Use only the URL to the .gz file to make the custom track.

The BED format used by WashU Epigenome Browser:

1. chromosome name
2. start coordinate
3. stop coordinate
4. Name (if absent, use dot)
5. ID (unique non-negative integer)
6. Strand (+/-/.)

Prepare custom track of numerical data

0	Make sure you have the tabix program installed. You can download the latest source and compile: http://sourceforge.net/projects/samtools/files/tabix/ Or if you're using Ubuntu operating system, install it using apt-get: $ apt-get install tabix You should have both tabix and bgzip programs available on your computer.
1	Skip this step if your file is bedGraph format. For bigWig files... Rrun the command bigWigToBedGraph in UCSC genome browser tool set and convert the bigWig file to a bedgraph text file. For wiggle files... Convert them into bedgraph text files. Only a few lines of code is needed for this task. Or if you really hate coding, you can convert the wiggle file to bigWig format using wigToBigWig (also from UCSC genome browser tool set), then do bigWigToBedGraph.
2	Compress the bedgraph text file: $ bgzip input.bedgraph The old file is gone and a new file "input.bedgraph.gz" is there instead.
3	Build tabix index of the compressed bedgraph file $ tabix -p bed input.bedgraph.gz The "input.bedgraph.gz" is untouched but an index file "input.bedgraph.gz.tbi" is generated.
4	Display this file as a custom bedgraph track on WashU Genome Browser. Put the .gz and .gz.tbi files on the SAME directory on your web server. Use only the URL to the .gz file to make the custom track.

v7 major update - Long Range interaction view, SVG output

It's been quite a while since our last post in June. We've been busy preparing some big updates on our dear Epigenome Browser, and this morning we're very happy to deploy them on our public server so all of our dear users could benefit.

Long range genome interaction data visualization

The "long range genome interaction" data sets, as those generated by 5C, Hi-C, and ChIA-PET, capture 3-dimensional chromatin arrangement in cell nucleus. This type of data is very promising in improving our interpretation of high-throughput genomics assay results (e.g. TF ChIP-Seq, histone mark ChIP-Seq), and more importantly understanding how eukaryotic genomes function as nonlinear systems.

Now you can explore the long-range interaction data sets using our Browser! Just click the following link to see it in action:

http://epigenomegateway.wustl.edu/browser/?genome=hg19&coordinate=chr7:26663835-28123541&gftk=IMR90_40kb_hindIII_combined,trihm,wgEncodeGisChiaPetK562CtcfInteractionsRep1,arc,refGene,full&hmtk=GSM521898,GSM521897,GSM521895,GSM521901,GSM469970,GSM521900,GSM521899,GSM788085_1,GSM733692_1,GSM608165_1,GSM945298_1,GSM945279_1,GSM945165_2,GSM945299_1,GSM945279_2,GSM945278_1,GSM945278_2,GSM945298_2,GSM945297_1,GSM945299_2,GSM733680_1,GSM945165_1,GSM945297_2,GSM733651_1,GSM521911,GSM521909,GSM733653_1,GSM521887,GSM469967,GSM469966,GSM521889,GSM469968,GSM733656_1,GSM945228_1,GSM608167_1,GSM945228_2,GSM733658_1,GSM521912,GSM469973,GSM521914,GSM521913,GSM469974,GSM733778_1,GSM607494_1,GSM733776_1&metadata=Histone%20Mark,11310,14018

This humongous URL yields a view with two long range interaction tracks and a set of histone mark tracks. With a few twists you can achieve a view like the following screen shot:

The triangular heatmap shows data from a Hi-C assay on IMR90 cells (Dixon JR, Bing Ren,Nature 485(7398):376-80).

The arcs shows data from a ChIA-PET assay on K562 cells (ENCODE Project data).

The bunch of histone mark tracks are active/repressive histone marks on IMR90 and K562 alike. Most of them are obtained from ENCODE project.

The region on chr7 contains the HOXA gene cluster.

We are busy preparing a manuscript for this exciting new update, and the above example constitutes part of a figure in the manuscript.

We invite our users to explore this function (tell me any bugs, xzhou82 AT gmail). Some helpful tips are available in a short chapter from the user manual: http://epigenomegateway.wustl.edu/browser/manual/#c-c

Presently, 44 long-range assay tracks for human, and 14 for mouse are available through our Browser, all of which are public data sets. New ones will be added whenever they are available.

SVG output

After so many earnest requests, the high-quality Browser Shot output is finally implemented. To do it, click "Apps" button in the small toolbox and select SVG option:

The generated SVG file can be viewed in your web browser. The file is usually large so please be patient while it's been transferred. Firefox and Chromium show no problem at displaying such files. With Chromimium you can print the SVG file to a PDF file.

The SVG file output function is totally different with UCSC's PDF/PS output function. Everything is done on client-side, no server-side rendering is involved.

This function is still a prototype. Let me know if it breaks. I'm still working to enable SVG outputs for the Bird's Eye View and the Companion panel from the long-range track view.

We sincerely recommend the Chromium web browser (http://www.chromium.org/Home), it is absolutely free, and available for all platforms. Epigenome Browser loves it!