Hi Brooke,
Thank you very much for your immediate reply.
I have a few more questions on the ENSEMBL transcripts that I downloaded from
UCSC browser using "Tables" tab and would appreciate your feedback when you
have a chance:
1. Are the ENSEMBL transcripts on chr M (Mitochondria) already mapped to rCRS
chrM when someone uses the "Tables" tab on UCSC genome browser to download
these transcripts?
2. I am aware of the note given on UCSC website on chrM:
Note on chrM
Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion
sequence (represented as "chrM" in the Genome Browser) has been replaced in
GenBank with the recordNC_012920. We have not replaced the original
sequence, NC_001807, in the hg19 Genome Browser. We plan to use the Revised
Cambridge Reference Sequence (rCRS) in the next human assembly release.
My question is:
a. Does this note only apply to the genomic sequence? or
b. Does it also apply to the ENSEMBL transcripts on UCSC genome browser? Can
you please explain your answer to me in detail? I really want to understand
this.
The reason I am asking this is because the ENSEMBL annotation I see on UCSC
browser seems to be for the rCRS version. However I am not sure.
You will notice that in the old chrM (NC_001807) the first
transcript starts at position 579.
In the new rCRS chrM (NC_012920), transcript starts at 577 also this is
displayed in UCSC genome browser as
well.
Please see the 3 links below and attached figures .
http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=248088223&db=hg19&position=chrM%3A577-647
http://www.ncbi.nlm.nih.gov/nuccore/NC_001807.4?report=genbank
http://www.ncbi.nlm.nih.gov/nuccore/NC_012920
Thank you,
Laura
________________________________
From: Brooke Rhead <[email protected]>
To: Laura Smith <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Friday, March 16, 2012 2:41 PM
Subject: Re: [Genome] ensemble version
Hi Laura,
For future reference, you can tell which Ensembl version is currently being
displayed in the Ensembl Genes track by turning the track on in the Genome
Browser. There will be a label above the items in the track (currently it says
"Ensembl Gene Predictions - Ensembl 65"). Another way to find it is to click
on any track item. The Ensembl version will be displayed at the top of the
page, for example: "Ensembl Genes (ENST00000342992 - Ensembl 65)."
The information you found in the release log is correct: you would have
retrieved Ensembl version 62 data on 6/23/11. (Ensembl version 63 was released
on 30 Sep 2011.)
> Also, when I click on this webpage on the link for "ensemble version
> 62", it takes me to ensemble version 65. Is this a bug?
This is not exactly a bug. We generally only maintain one version of a track
on the Genome Browser, and any link on the Release Log page will take you to
that track. The information of what data was released on what date remains the
same, however.
Regarding the RefSeq track: the RefSeq track is updated daily in the Genome
Browser. So, you would have downloaded whatever RefSeq Genes were available
from Genbank as of 6/23/2011.
If you have further questions, please contact us again at [email protected].
--
Brooke Rhead
UCSC Genome Bioinformatics Group
On 3/16/12 9:06 AM, Laura Smith wrote:
> Hi,
>
> Can you please tell me which version of ensemble (the latest) was
> available on ucsc browser website by default from table view on
> 06/23/2011?
>
> Also can you please tell me which version of refseq (the latest) was
> on UCSC website as of 06/23/2011?
>
> The reason I am askign is because we have downloaded the refseq and
> ensemble transcripts from the ucsc genome browser website on
> 06/23/2011, however we do not know which version of ensemble and
> refseq downloaded corresponds to as there were no information in the
> files or on the website. We are sure we downloaded the latest ones
> available from table view, but we don't know which versions they
> correspond to.
>
> I found the following link on your website:
>
> http://genome.ucsc.edu/goldenPath/releaseLog.html#hg19
>
> Also, when I click on this webpage on the link for "ensemble version
> 62", it takes me to ensemble version 65. Is this a bug?
>
> I would appreciate your feedback.
>
> Laura _______________________________________________ Genome maillist
> - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
