hg19.gbstatus and hg19.gbCdnaInfo have outdated refseq versions
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Simmon, Keith
May 26, 2016, 10:15:42 AM5/26/16
to gen...@soe.ucsc.edu
Hi,
It appears that the ‘gbStatus' and ‘gbCdnaInfo' tables are out-of-date compared to the refGene Table for hg19.
The RefGene mappings appear to correlate with current refseq versions, for example NM_001301016 and NM_212492 are listed as version 2 on NCBI, which were updated at NCBI on 28-APR-2016, and 18-MAR-2016, respectively.
However gbStatus and gbCdnaInfo, report 1 as the transcript version.
Could you confirm that gbStatus and gbCdnaInfo are being updated for hg19?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Here is an example
~~~~~~~~~
RefGene output for NM_013354 FROM 2 MONTHS AGO [REPORT AS VERSION 4]
112 NM_007040 chr19 + 41770226 41813597 41770408 41812470 15 41770226,41774127,41777986,41779886,41782063,41784981,41787067,41798149,41800242,41800462,41807440,41808569,41809876,41811580,41812353, 41770703,41774250,41778140,41779960,41782203,41785081,41787180,41798416,41800365,41800591,41807609,41808854,41810166,41811772,41813597, 0 HNRNPUL1 cmpl cmpl 0,1,1,2,1,0,1,0,0,0,0,1,1,0,0,
~~~~~~~~
CURRENT MAPPINGS for NM_013354 [looks like this is from version 5, BUT STILL LISTED AS VERSION 4 in gbStatus and gbCdnaInfo]
112 NM_007040 chr19 + 41770078 41813688 41770408 41812470 15 41770078,41774127,41777986,41779886,41782063,41784981,41787067,41798149,41800242,41800462,41807440,41808569,41809876,41811580,41812353, 41770703,41774250,41778140,41779960,41782203,41785081,41787180,41798416,41800365,41800591,41807609,41808854,41810166,41811772,41813688, 0 HNRNPUL1 cmpl cmpl 0,1,1,2,1,0,1,0,0,0,0,1,1,0,0,
~~~~~~~ REFSEQ UPDATED THIS transcript in APR 2016 ~~~~~~~~
LOCUS NM_007040 4136 bp mRNA linear PRI 28-APR-2016
DEFINITION Homo sapiens heterogeneous nuclear ribonucleoprotein U like 1
(HNRNPUL1), transcript variant 1, mRNA.
ACCESSION NM_007040
VERSION NM_007040.5 GI:1007389160
KEYWORDS RefSeq.
~~~~~ QUERY TO UCSC SHOWNING VERSION 4 as transcript version ~~~~~~~~~~~~~~~~~
SELECT * FROM refGene as rg JOIN gbStatus as gs ON (rg.name = gs.Acc) JOIN gbCdnaInfo as c ON (rg.name = c.acc) WHERE rg.name='NM_007040';
| 112 | NM_007040 | chr19 | + | 41770078 | 41813688 | 41770408 | 41812470 | 15 | 41770078,41774127,41777986,41779886,41782063,41784981,41787067,41798149,41800242,41800462,41807440,41808569,41809876,41811580,41812353, | 41770703,41774250,41778140,41779960,41782203,41785081,41787180,41798416,41800365,41800591,41807609,41808854,41810166,41811772,41813688, | 0 | HNRNPUL1 | cmpl | cmpl | 0,1,1,2,1,0,1,0,0,0,0,1,1,0,0, | NM_007040 | 4 | 2015-02-15 | mRNA | RefSeq | native | 73218352 | 1 | 66 | 2014.0722 | 69 | full | 69 | full | 2015-03-17 20:06:28 | 73218352 | NM_007040 | 4 | 2015-02-15 | mRNA | 0 | 452 | 448 | 0 | 0 | 0 | 0 | 0 | 0 | 428619 | 2079054 | 399325 | 63004 | 436137 | 310996 | 666875870 | mRNA |
Thanks Keith
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It appears that the ‘gbStatus' and ‘gbCdnaInfo' tables are out-of-date compared to the refGene Table for hg19.
The RefGene mappings appear to correlate with current refseq versions, for example NM_001301016 and NM_212492 are listed as version 2 on NCBI, which were updated at NCBI on 28-APR-2016, and 18-MAR-2016, respectively.
However gbStatus and gbCdnaInfo, report 1 as the transcript version.
Could you confirm that gbStatus and gbCdnaInfo are being updated for hg19?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Here is an example
~~~~~~~~~
RefGene output for NM_013354 FROM 2 MONTHS AGO [REPORT AS VERSION 4]
112 NM_007040 chr19 + 41770226 41813597 41770408 41812470 15 41770226,41774127,41777986,41779886,41782063,41784981,41787067,41798149,41800242,41800462,41807440,41808569,41809876,41811580,41812353, 41770703,41774250,41778140,41779960,41782203,41785081,41787180,41798416,41800365,41800591,41807609,41808854,41810166,41811772,41813597, 0 HNRNPUL1 cmpl cmpl 0,1,1,2,1,0,1,0,0,0,0,1,1,0,0,
~~~~~~~~
CURRENT MAPPINGS for NM_013354 [looks like this is from version 5, BUT STILL LISTED AS VERSION 4 in gbStatus and gbCdnaInfo]
112 NM_007040 chr19 + 41770078 41813688 41770408 41812470 15 41770078,41774127,41777986,41779886,41782063,41784981,41787067,41798149,41800242,41800462,41807440,41808569,41809876,41811580,41812353, 41770703,41774250,41778140,41779960,41782203,41785081,41787180,41798416,41800365,41800591,41807609,41808854,41810166,41811772,41813688, 0 HNRNPUL1 cmpl cmpl 0,1,1,2,1,0,1,0,0,0,0,1,1,0,0,
~~~~~~~ REFSEQ UPDATED THIS transcript in APR 2016 ~~~~~~~~
LOCUS NM_007040 4136 bp mRNA linear PRI 28-APR-2016
DEFINITION Homo sapiens heterogeneous nuclear ribonucleoprotein U like 1
(HNRNPUL1), transcript variant 1, mRNA.
ACCESSION NM_007040
VERSION NM_007040.5 GI:1007389160
KEYWORDS RefSeq.
~~~~~ QUERY TO UCSC SHOWNING VERSION 4 as transcript version ~~~~~~~~~~~~~~~~~
SELECT * FROM refGene as rg JOIN gbStatus as gs ON (rg.name = gs.Acc) JOIN gbCdnaInfo as c ON (rg.name = c.acc) WHERE rg.name='NM_007040';
| 112 | NM_007040 | chr19 | + | 41770078 | 41813688 | 41770408 | 41812470 | 15 | 41770078,41774127,41777986,41779886,41782063,41784981,41787067,41798149,41800242,41800462,41807440,41808569,41809876,41811580,41812353, | 41770703,41774250,41778140,41779960,41782203,41785081,41787180,41798416,41800365,41800591,41807609,41808854,41810166,41811772,41813688, | 0 | HNRNPUL1 | cmpl | cmpl | 0,1,1,2,1,0,1,0,0,0,0,1,1,0,0, | NM_007040 | 4 | 2015-02-15 | mRNA | RefSeq | native | 73218352 | 1 | 66 | 2014.0722 | 69 | full | 69 | full | 2015-03-17 20:06:28 | 73218352 | NM_007040 | 4 | 2015-02-15 | mRNA | 0 | 452 | 448 | 0 | 0 | 0 | 0 | 0 | 0 | 428619 | 2079054 | 399325 | 63004 | 436137 | 310996 | 666875870 | mRNA |
Thanks Keith
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The information transmitted by this e-mail and any included
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recipient. The information contained in this message is confidential
and may constitute inside or non-public information under
international, federal, or state securities laws, or protected health
information and is intended only for the use of the recipient.
Unauthorized forwarding, printing, copying, distributing, or use of
such information is strictly prohibited and may be unlawful. If you
are not the intended recipient, please promptly delete this e-mail
and notify the sender of the delivery error or you may call ARUP
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Matthew Speir
May 26, 2016, 11:51:01 AM5/26/16
to Simmon, Keith, gen...@soe.ucsc.edu
Hello Keith,
Thank you for your question about the gbStatus and gbCdnaInfo tables.
We are in the process of replacing these tables with shared tables in
our "hgFixed" database. These two tables are part of a set of metadata
tables that had previously been replicated across all of our assembly
databases. We have moved these tables to a shared database called
hgFixed and have ceased updating these tables in the individual assembly
databases. We have yet to drop these tables from the various assembly
databases but plan to do that soon.
You can download the gbStatus and gbCdnaInfo tables from our download
server here:
http://hgdownload.soe.ucsc.edu/goldenPath/hgFixed/database/
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.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about the gbStatus and gbCdnaInfo tables.
We are in the process of replacing these tables with shared tables in
our "hgFixed" database. These two tables are part of a set of metadata
tables that had previously been replicated across all of our assembly
databases. We have moved these tables to a shared database called
hgFixed and have ceased updating these tables in the individual assembly
databases. We have yet to drop these tables from the various assembly
databases but plan to do that soon.
You can download the gbStatus and gbCdnaInfo tables from our download
server here:
http://hgdownload.soe.ucsc.edu/goldenPath/hgFixed/database/
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.
Matthew Speir
UCSC Genome Bioinformatics Group
Keith Simmon
May 26, 2016, 1:19:31 PM5/26/16
to gen...@soe.ucsc.edu
Thank you Matthew,
Was the 'gbStatus' table renamed in hgFixed. I do not see it?
Keith
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Cath Tyner
May 26, 2016, 5:18:01 PM5/26/16
to Keith Simmon, UCSC Genome Browser Public Help Forum
Hello Keith,
Our apologies for the confusing information - you are correct, the gbStatus table is not located in the hgFixed database. If you could reply and give more detail about what information you are specifically looking for from gbStatus, we may be able to help you find what you need from other tables. If this would be helpful, you can post a reply in this thread, or you are welcome to email me off-list if the information is confidential.
* Unsubscribe: Email genome-announ...@soe.ucsc.edu
Our apologies for the confusing information - you are correct, the gbStatus table is not located in the hgFixed database. If you could reply and give more detail about what information you are specifically looking for from gbStatus, we may be able to help you find what you need from other tables. If this would be helpful, you can post a reply in this thread, or you are welcome to email me off-list if the information is confidential.
Thank you again for your inquiry and for using the UCSC Genome Browser.
Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:
* Confidential/private data help: Email
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Enjoy,
Cath Tyner
May 27, 2016, 11:37:25 AM5/27/16
to Keith Simmon, UCSC Genome Browser Public Help Forum
Hi Keith,
Yes, gbStatus.modDate and gbCdnaInfo.moddate contain the same values. It's my understanding that our engineer team is currently evaluating the best place for gbStatus (hgFixed or the assembly databases).
Thank you again for your inquiry and for using the UCSC Genome Browser.
Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:
* Confidential/private data help: Email
genom...@soe.ucsc.eduUCSC Genome Browser Announcements List (email alerts for new data & software):
* Subscribe: Email genome-annou...@soe.ucsc.edu * Unsubscribe: Email genome-announ...@soe.ucsc.edu
Enjoy,
On Thu, May 26, 2016 at 3:41 PM, Keith Simmon <ke....@gmail.com> wrote:
No Problem Cath,The main info I want is the refseq version. I can get this from the 'gbCdnaInfo' table. I also have been pulling the 'modDate' [last modified date] and the 'time' [time that this entry was inserted]. Is the modDate in 'gbCdnaInfo' the same.Thanks for your help.Keith
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