bed12 support?

asked 2016-07-25 09:02:41 -0600

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Hi,

I knew the Golden Helix GenomeBrowser for a long time, but has been using igv for my research.

Few days ago I tried GenomeBrowser and found it carry so much more feature I liked. So immediately I decided to use it as my main replacement tool for iGV.

However, I found it does not support bed12 format, basically it parses it as bed3 format and shows only single block instead of multiple blocks.

I would highly appreciate if this feature would be considered adding to the next release, or if it was available let me know. I have been playing with the controls for a while and did not seem to find and parameters to turn bed12 on.

Thank you for the awesome tool.

Shuoguo

answered 2016-07-25 16:29:16 -0600

Jami Bartole
201 ●3 ●3 http://www.goldenhelix.co...

Hi Shuoguo,

I am glad you have been enjoying GenomeBrowse.

The current BED format supported in GenomeBrowse is focused around displaying "generic" intervals that have just a start, stop and potentially a label and color defined in the data. Does your BED file contain transcript data, if so they we recommend getting the same data available in GTF as GenomeBrowse can easily parse this for visualization of the individual transcripts.

Another option is to load the BED file into our Convert Wizard (select File > Add then click Convert in the lower left corner) which will allow you to adjust some of the visualization options of the raw data. If you can provide an example of a plot that shows the data in your expected format that would be most useful in determining where GenomeBrowse can be updated with that feature.

Let me know how I can help you further.

Thanks, Jami...

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