Downloading the UCSC gene annotation files

Question

[kaczor.karolina]

Hello,

Do you know maybe how to download the UCSC annotation files (with genomes of Campylobacter jejuni, Campylobacter jejuni 81-176, Campylobacter jejuni RM1221) from UCSC browser?

[GenoMax]

Cross-posted: http://seqanswers.com/forums/showthread.php?t=67515

Answer 1

[Alex Reynolds]

Visit the UCSC Table Browser for Archaea and pick your genome and assembly from the respective pull-down menus.

Select the region of interest, group and track for the annotations of interest, select the output format and output name, and finally click get output to begin a data download.

There may also be options to retrieve database tables via mysql. Try posting your question to the UCSC Genome Browser discussion group to see if this is available.

Answer 2

[CandiceChuDVM]

The last answer of this post can provide you option details in the UCSC table browser:
How to download Gene annotations.gtf file for Drosophila melanogaster

[GenoMax]

Not applicable in case of original question. The link in the answer you point to is only applicable for eukaryotic/special genomes available in UCSC.

@Alex has the correct link for prokaryotic UCSC table browser in his answer.