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Old 02-09-2011, 11:59 PM   #1
Location: Japan

Join Date: Oct 2010
Posts: 52
Default Displaying DGE (bed-files) with Integrative Genomics Viewer

I have digital gene expression data in bed-format.

One type of file would be bed-files where each entry corresponds to one sequenced tag.

Another type of file would be bed-files where each entry corresponds to a "cluster" of tags, and the score-field of the bed-file corresponds to the expression level of that cluster.

I want to display this data in the IGV browser from broad institute.

I can load the data, but I see the data only displayed in the form of regions on the genome. However, what I want to see is some kind of barchart so that I can clearly see where and *how many* of my tags align. I.e. I want to see expression levels in a quantitative way (bar chart, graph...).

How can I set the display options accordingly?

Or, should I not use bed-format in the first place, then which format would you recommend?
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Old 09-01-2011, 07:58 PM   #2
Jim Robinson
Location: Boston, MA

Join Date: May 2009
Posts: 75

Well, this is so old I hestitate to respond. For the sake of "googlers" everywhere I will, however. Hopefully you got an answer to this long before now.

A large number of file formats are supported, but they fall into 2 categories, (1) features, and (2) data. You need a data format. The easiest format if you already have bed files is UCSC's "bedgraph". Just drop the strand column and you have it. Name the file to end with ".bedgraph" and you are done. It should now display as a barchart by default, although you can change this to a heatmap if you like.

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dge, igv, visualization

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