RN6... what's going on

[Sumner Magruder]

Hi,

What is going on with the RN6 annotation?

The ensemble transcript IDs seem to be incorrect and match to the gene ids…

i.e.

Transcript ID Gene ID

ENSRNOT###########.# ENSRNOT###########.#

It is obvious that the gene id is incorrect given the T, and Ensembl’s biomart files are all devoid of the appended .#

Please help.

Thanks,

Sumner

“My strength lies solely in my tenacity”

~ Louis Pasteur

[Christopher Lee]

Hi Sumner,

Thank you for your question about rn6 Ensembl Gene annotations. Is it possible for you to share a few example transcripts or a session where you are seeing this issue? When I click on any of the items in the Ensembl track in this session:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=rn6EnsemblTranscriptIds

The description page correctly lists both the ENSRNOT and ENSRNOG identifiers.

Additionally, when I grab data from the Table Browser I also see both transcript ID's and gene ID's:

#rn6.ensGene.name    rn6.ensGene.name2    rn6.ensGtp.gene    rn6.ensGtp.transcript    rn6.ensGtp.protein
ENSRNOT00000044187.4    ENSRNOG00000046319.3    ENSRNOG00000046319.3    ENSRNOT00000044187.4    ENSRNOP00000050608.3
ENSRNOT00000072186.1    ENSRNOG00000046319.3    ENSRNOG00000046319.3    ENSRNOT00000072186.1    ENSRNOP00000065675.1
ENSRNOT00000072360.2    ENSRNOG00000047964.2    ENSRNOG00000047964.2    ENSRNOT00000072360.2    ENSRNOP00000064396.2
ENSRNOT00000073546.3    ENSRNOG00000050370.3    ENSRNOG00000050370.3    ENSRNOT00000073546.3    ENSRNOP00000065611.2

The number after the . is the version of the transcript from Ensembl. Ensembl displays these numbers when you are looking at the description page for an individual transcript on their site. For example the ENSRNOT00000044187.4 transcript leads to the following page at Ensembl:
http://uswest.ensembl.org/Rattus_norvegicus/Transcript/Summary?g=ENSRNOG00000046319;r=1:396700-409676;t=ENSRNOT00000044187

where in the "Summary" section you can see the following information:

"Ensembl version                ENSRNOT00000044187.4"

I hope this was helpful, please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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[Chris Villarreal]

Hello Sumner,

Any GTF output from the UCSC Table Browser will have the issue with
matching gene and transcript IDs. If you want output with gene IDs,
you will need to use the genePredToGtf utility. For more information
on converting genes from genePred to GTF format, please see the
following page:
http://genomewiki.cse.ucsc.edu/index.php/Genes_in_gtf_or_gff_format.

I hope this is helpful. If you have any further questions, please

reply to gen...@soe.ucsc.edu. 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.

-Chris V
UCSC Genome Browser

[Chris Villarreal]

Hello Sumner,

To download the Kent source tools please visit
http://hgdownload.soe.ucsc.edu/admin/exe/ and follow these steps:

1. Select your operating system. To determine which set of binaries to
download, type "uname -a" on the command line to display your machine
type.

2. Select the genePredToGtf file to begin the download.

You will need to use your command line to run the utility.

I hope this is helpful. If you have any further questions, please
reply to gen...@soe.ucsc.edu. 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.

-Chris V
UCSC Genome Browser

On Thu, Oct 20, 2016 at 12:08 AM, Sumner Magruder <mag...@live.com> wrote:
> Hi Chris,
> when did this take effect?
> I have done what I have shown you in the past and it worked fine.
> What are Kent utilities and how can I install them so that I can follow the
> guide on the wiki?

> Thanks,
> Sumner
>
> “My strength lies solely in my tenacity”
> ~ Louis Pasteur
>