viewing BED Graph files on the IGB

Question

[akivab2]

For some reason I can't view bedgraph files on the IGB. specifically I am referring to files of data of the Arabidopsis genome.

Has anybody else had this issue? Does anyone have a solution to this?

Thank you

[zx8754]

Do you mean IGV?

[akivab2]

I am actually referring to the IGB (integrated genome browser).

Answer 1

[Ann]

Hi,

Could you post a link to the file or email a sample to one of the IGB team? We would be happy to take a look.

You can send it to [e-mail]

Regarding bedgraph:

You should be able to load a bedgraph file into IGB in the usual way:

• Select File > Open
• Choose your file
• Zoom in (Many options for zooming: use slider, click "+" button, double-click a gene model, or click-drag across the sequence axis)
• Click Load Data button (top right)

However, if your file is very large, it would be good to sort, compress and index it using bgzip and tabix before loading it into IGB. If you do that, then you can load just a part of your file into IGB and the load will be much faster.

Using bgzip and tabix:

sort -k1,1 -k2,2n FILE.bedgraph | bgzip > FILE.bedgraph.gz
tabix -s 1 -b 2 -e 3 FILE.bedgraph.gz

The first commands creates a sorted, indexed, compressed bedgraph file - FILE.bedgraph.gz. The second command creates an index for it - FILE.bedgraph.gz.tbi. Make sure you always store the index (.tbi file) in the same directory as the bedgraph.gz file.

Tips:

• Use file extension "bedgraph" to ensure IGB recognizes the file format
• Use functions in the Graph tab to change how the graph looks (You can change the scale, change the visible range, view the graph as a heat map, change color, copy, and more.)