Rabail Zehra

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May 26, 2015, 11:20:08 AM5/26/15

to gen...@soe.ucsc.edu

Hi,

I am interested in finding out about pre-computed MKAR values for the human genome (hg19) at UCSC.. Can you please guide me with that?

Jonathan Casper

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May 29, 2015, 7:31:50 PM5/29/15

to Rabail Zehra, gen...@soe.ucsc.edu

Hello Rabail,

Thank you for your question about locating MKAR values for the hg19 human genome assembly. Unfortunately, we do not appear to have any MKAR data. The little information I found online suggests that some custom tracks containing MKAR data were created for the hg18 genome assembly; if you are able to locate the data files for those tracks, you should be able to translate them to the hg19 assembly using our LiftOver tool at http://genome.ucsc.edu/cgi-bin/hgLiftOver. If there is a specific dataset that you have in mind, you may also be able to contact the author and see if it is still available somewhere.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

On Sun, May 24, 2015 at 11:13 PM, Rabail Zehra <rabai...@gmail.com> wrote:

Hi,

I am interested in finding out about pre-computed MKAR values for the human genome (hg19) at UCSC.. Can you please guide me with that?

--

雨泽天下

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Jun 1, 2015, 12:27:07 PM6/1/15

to genome

Dear professor,
I am a student in Chinese and I want to use txCdsPredict score to predict whether my transcrits is protein-coding or
non-coding, but I could not found the txCdsPredict in UCSC. Can you tell me how to find it and use it.

Thank you sincerely.
Jian Fang

Steve Heitner

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Jun 1, 2015, 1:52:28 PM6/1/15

to 雨泽天下, genome

Hello, Jian.

This program is located in the kent source tree at http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/hg/txCds. Please also see the previously-answered mailing list question at https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/0yP-Ez2uQ0Y/7Xt9dUii8QgJ. Run the tool from the command line without parameters to see the usage statement.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

---
Steve Heitner
UCSC Genome Bioinformatics Group

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Sabine Fondel

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Jun 11, 2015, 12:18:15 PM6/11/15

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Dear technical supprt,

in the past I created my primers using

UCSC Genome Browser on Human Dec. 2013 (GRCh38/hg38) Assembly

But today I can't find the tool "microsatellite" under the Icon REPEATS.

Where can I find it on this page?

Thanks for helping

Sabine

Steve Heitner

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Jun 11, 2015, 1:27:11 PM6/11/15

to Sabine Fondel, gen...@soe.ucsc.edu

Hello, Sabine.

The Microsatellite track doesn’t yet exist on hg38 on our public site, but it does exist on hg19. Are you certain you weren’t using hg19?

We do have plans to release the Microsatellite track on hg38 and it does currently exist on our preview server. If you were indeed using hg38, you could only have accessed the Microsatellite track through our preview server at http://genome-preview.ucsc.edu/. Please note that items on our preview server are still in development and subject to change at any time.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.