An Hsu
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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

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

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Last updated: May 29 '14

bed file format for display transcripts

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