Question: Is There A Program For Viewing Bed Files And Wig Files?
0
gravatar for KCC
8.1 years ago by
KCC4.0k
Cambridge, MA
KCC4.0k wrote:

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.

bed wiggle • 14k views
ADD COMMENTlink written 8.1 years ago by KCC4.0k
7
gravatar for Istvan Albert
8.1 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

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?
ADD COMMENTlink modified 5 weeks ago by RamRS24k • written 8.1 years ago by Istvan Albert ♦♦ 81k

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

ADD REPLYlink written 8.1 years ago by Lars Juhl Jensen11k
3
gravatar for brentp
8.1 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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.

ADD COMMENTlink written 8.1 years ago by brentp23k
2

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.

ADD REPLYlink written 8.1 years ago by Bert Overduin3.6k

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

ADD REPLYlink written 8.1 years ago by brentp23k
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