WashU Epigenome Browser

Custom tracks

✘

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bedGraph

quantitative data

bigWig

quantitative data

BED

annotation data

BED ⋒

long-range interaction data

SAM

read alignment data

DataHub

batch submission

Registry (0)

bedGraph file must be compressed by bgzip and indexed by tabix. Learn more ↗

bedGraph file URL

The index file must be accessible from the same path
If bedgraph file name is "input.gz", the index file name must be "input.gz.tbi"

Track name

optional

example

bigWig↗ file URL

Track name

optional

example

bigBed files are no longer supported, use BED files instead (tabix indexed). Learn more ↗

BED file URL

The index file must be accessible from the same path
If bed file name is "input.gz", the index file name must be "input.gz.tbi"

Track name

Display mode

optional

example

Please prepare the long-range interaction data according to the format specification Learn more ↗

Data file URL

The index file must be accessible from the same path
If interaction data file name is "input.gz", the index file name must be "input.gz.tbi"

Track name

Display mode

Positive score threshold

only applies to items with scores ≥ 0, excludes items with scores below the threshold

Negative score threshold

only applies to items with scores ≤ 0, excludes items with scores above the threshold

optional

example

BAM files are not supported at the moment, please use SAM files instead (tabix indexed). Learn more ↗

SAM file URL

The index file must be accessible from the same path
If bed file name is "input.gz", the index file name must be "input.gz.tbi"

Track name

Display mode

optional

example

DataHub accomodates tracks of all types, along with metadata annotation

help_↗ example

Click 'Delete' to remove permanently

Quantitative track (0)

Annotation track (0)

Long range interaction track (0)

Read alignment track (0)

Primary criterion

Secondary criterion

♪	Your web server must support byte-range request Dropbox or other file sharing services cannot be used

Gene Plot

✘

0 - Genes and regions

Or, use an annotation track to supply genomic regions:

The annotation track should be already displayed in the browser.
When an annotation track is selected, text area inputs are ignored.
Refer to these instructions to prepare a custom annotation track.

1 - Data track

only numerical tracks can be used, including bigWig and bedGraph

2 - Graph type

Quartiles & extremes

All genes and genomic intervals are tiled together, genes are always from 5' to 3', relative to their strands. Track data of each gene are summarized into fixed length vectors, and median value over each data point is plotted.

Number of data points

Line width median curve image width height
other curves use lighter color
plot average values

Spaghetti

One line is plotted for each gene or item, genes are always from 5' to 3', relative to their strands. Track data of each gene and item are summarized into equal length vectors.

Number of data points

Line width line color image width height

Gene parts

Profiles of gene parts (3 kb promoter, 5' UTR, exons, introns, 3' UTR) will be plotted as separate curves, in the same fashion as first plot type (only applies to genes, genomic coordinates will be skipped)

Number of data points for each segment type

Line width image width height

promoter 5' UTR exons introns 3' UTR

Above colors are for median curves. Lighter color will be used for other curves. whisker range outlier ?
plot average values

Clustering

Run hierarchical or K-means clustering analysis on genes, and explore result through its interactive features.

Number of data points

Clustering method

distance metric agglomeration number of clusters

Row height plot width of data points
use global min/max positive value negative value (white for zero baseline)

3 - Rendering method

- R software generates box plots in form of still PNG images
- Google Chart generates interative line plots

You don't need to make selection for this type of graph

Firefox user: after first time using this function, the image is probably not updating anymore. This is because your browser is doing a too good job caching stuff. Follow this note to turn off caching so you can see the image updating.
If you don't see the image after clicking 'Make plot' button, it's likely that you're running into 'URL too long' problem. Try reducing number of genes and/or number of data points and do again.

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Get data

genes with 0 standard deviation are excluded from clustering analysis