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bed file format for display transcripts

asked 2014-05-28 22:49:11 -0600

An Hsu gravatar image

I try to use the bed file format to display transcripts with my own cases. I follow the bed file format in the UCSC genome browser. It works on UCSC genome brower, but fails in Golden Helix GenomeBrowse. I try to figure out, and I find that Golden Helix GenomeBrowse only can identify the bed file as a interval source and the other information such as, thickstart, thickend and blockcount would be identified as value type. could you provide a bed file as example to me. Thanks a lot.

An Hsu PhD student Chang Gung University, Taiwan

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answered 2014-05-29 15:18:05 -0600

Hey An Hsu,

The BED format support in GenomeBrowse is focused around displaying "generic" intervals that have just a start, stop and potentially a label and color defined in the data.

If you actually have transcript data you want to display, I would suggest saving it out of UCSC in GTF format. The UCSC table browser should have a GTF export option.

Then our convert wizard will detect it as transcript data and you can visualize it as a Gene track.

Hope that helps, Gabe

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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.


Asked: 2014-05-28 22:49:11 -0600

Seen: 19,119 times

Last updated: May 29 '14