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BED file support

asked 2012-09-27 11:41:05 -0600

tnt 1 gravatar image

I see it's easy to put a BAM file into GenomeBrowse but am wondering if a custom interval file can be added. I have a BED file of CNVs of interest and would like to make a track that looks exactly like the DGV track you have only for my data. Is it possible and if so what format can I use?

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answered 2013-05-30 11:02:30 -0600

We have released version 1.1.2 of GenomeBrowse which now includes support for reading sorted BED files directly! The "track" line is respected to support display name, coloring and the bedDetail format variant.

You can update to the newest version of GenomeBrowse by downloading the installer from our website.

Please see the Release Notes for version 1.1.2 for a full descriptions of what is now available.

Thanks, Jami...

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answered 2012-10-12 12:17:36 -0600

updated 2013-03-27 13:24:05 -0600

To expand on Jami's answer, although it's very enterprising to convert a BED file to BAM, the files have very different focuses on the types of data they support and the experience of viewing the converted data would be approximate at best.

Similarly, FASTA or GFF would not convert well to BAM. As Jami mentioned though, we plan on building built in support for converting all of these file types in the future.

For the moment, we are "bootstrapping" GenomeBrowse with the technology of SVS. This means for viewing annotation sources GenomeBrowse relies on annotations being converted to our efficient binary IDF file format.

SVS produces IDF files when converting BED, FASTA, GTF or any text file downloaded from the UCSC genome browser table viewer. GenomeBrowse is set up to auto-detect files that SVS converts, and they are ready to plot the next time you go to the Add dialog.

SVS is Golden Helix’s analysis product for a variety of workflows and is a commercial tool, you can request an evaluation of SVS through the evaluation request form.

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answered 2012-10-12 09:55:07 -0600

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I'm having a similar but slightly different problem. I have my file in bed format so I converted into bam format using bedToBam (Jami you can find the tools for that at My problem is that after I've converted it over and import into genomebrowse...the program crashes. Do you know if there needs to be specific header information? Or if there is another reason that the program is crashing which I can fix here?

Thanks ahead of time,


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Sara, I'm sorry to hear you ran into a crash. We are trying to collect examples of BAM files that do cause crashes.

Please email us at [email protected] if you would be willing to share the BAM file you created in a secure fashion.

Gabe Rudy ( 2012-10-12 12:05:22 -0600 )edit

answered 2012-09-27 11:44:02 -0600

We are currently working on implementing a tools in GenomeBrowse that would allow the user to add custom files not currently available in the software. Those files could come from a variety of file types including BED and other quantitative value type data.

Please see our website at the following link for specifics on upcoming features.

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Asked: 2012-09-27 11:41:05 -0600

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Last updated: May 30 '13