Ask Your Question

bed12 support?

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

this post is marked as community wiki

This post is a wiki. Anyone with karma >75 is welcome to improve it.


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.


edit retag flag offensive close merge delete

1 answer

Sort by ยป oldest newest most voted

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

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...

edit flag offensive delete link more
Login/Signup to Answer

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.

Question Tools

1 follower


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

Seen: 345 times

Last updated: Jul 25 '16