cutters table

[Mitch Hayes]

Hello,

I'm trying to find the cutters table (restriction enzyme mapping data --
REBASE) in the Table Browser.  It is present as a track in the Mapping
and Sequencing group in the Genome Browser
(http://www.genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=325535671&c=chr17&g=cutters).
I have tried looking both in the browser and in
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ without any
success. Any suggestions?


Thanks,

Mitch Hayes

School of Medicine and Public Health

UW-Madison

[Cath Tyner]

Hi Mitch,

Thanks for contacting the UCSC Genome Browser support team. Since this particular table is used by all assemblies, 

it's stored in the "hgFixed" database: hgFixed.cutters.

You can configure the Table Browser as follows:

For example, using hg38:

Here is an related support post with further details.

As you move forward, please feel free to respond to this forum at any time if our support team can provide further assistance, 

and please always feel free to search our mailing list archives for related posts.

Thank you for contacting the UCSC Genome Browser support team. 

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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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[Cath Tyner]

Hello again Mitch, 

Here are additional resources which may be helpful as well:

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/z7vaICqaY1g/Zv-cxQ-KEwAJ

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/EeGlFVIgGTA/uZKu1kREF1cJ

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

[Mitch Hayes]

Hi Cath,

Thanks for the information.  I didn't realize that the restriction sites were determined on the fly.  Ultimately, I decided to use restrict from EMBOSS to calculate the fragment lengths and then cat'd the results together from each of the chromosomes.

Thanks again,

Mitch