Hi Laura, Thank you for pointing out this issue. An updated ensGene table with the correct chrM entries has been placed on our test server:
http://genome-test.soe.ucsc.edu/cgi-bin/hgTables Please note that the data on this server hasn't been through our quality assurance process and is subject to change. If you have further questions, please don't hesitate to contact the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Laura Smith <[email protected]> Date: Tue, Mar 20, 2012 at 4:34 PM Subject: Re: [Genome] ensemble version To: Brooke Rhead <[email protected]> Cc: "[email protected]" <[email protected]> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
