Binary BED file?

[Dave Klipper]

Hello,

Does the UCSC Genome Browser read a BED file which is in a binary format?

I am familiar with BED files in the text format, but was given a binary file with a bed extension and told it could be read by your browser. But when I try it, I see an error that says the file format is unrecognized. 

Thank you very much for your time.

[Cath Tyner]

Hello Dave,

Thank you for using the UCSC Genome Browser and for contacting the support team for assistance with the bigBed file issue you are having. It sounds like you may have a indexed, binary "bigBed" file that is using an incorrect extension. If the file extension for your bigBed file is bigBed.bed, our software will expect that you are trying to load a bed file. Your bigBed file should have the appropriate extension, bigBed.bb. You should be able to rename your file and add the correct *.bb extension, and then try loading the custom track again. I have just tested this process and found that it works for me, but let us know if you have any problems.

Here are some resources that may be helpful to you:

1. bigBed Track Format (note that you can try to load some example bigBed files from this page)

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You will also need to make sure that your web server supports byte-range requests. For more information, please see this previously answered mailing list question

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At any time, you can visit our help forum and search the archives

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Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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