Is There A Program For Viewing Bed Files And Wig Files?

Question

[KCC]

Is there a program for viewing BED files and WIG files? From my own googling, it seems like there are websites that can do this, although I'm not sure how to use them.

Answer 1

[Istvan Albert]

This is one of those applications that are surprisingly hard to find comparisons of (google-ing often leads to many false paths), some that come to mind are:

Integrative Genomics Viewer: http://www.broadinstitute.org/igv/

Integrated Genome Browser: http://bioviz.org/igb/

Lightweigth Genome Viewer: http://lwgv.sourceforge.net/

The following Biostar question also have many good answers:

1. Next Generation Read Sequence Assembly Visualization Software
2. What Tools/Libraries Do You Use To Visualize Genomic Feature Data?

[Lars Juhl Jensen]

+1 for pointing out that this is hard to Google. I tried myself and failed.

Answer 2

[brentp]

I have found that IGV (linked by @Istvan) and the UCSC genome browser are the most full-featured and the easiest browsers to use.

• IGV is a java (or java webstart) application.

• UCSC is a web-based browser where you either upload your own data or tell it where to find data on your own server.

Both will support BED and WIG among other formats.

[Bert Overduin]

Ensembl (http://www.ensembl.org) also supports upload and attaching remote data for many different formats. For more detailed information please have a look at http://www.ensembl.org/info/website/upload/index.html.

[brentp]

Bert, thanks. Does Ensembl support bigbed/bigwig from another server?