genome | 21 Jul 19:23 2014

Digest for genome <at> soe.ucsc.edu - 5 updates in 4 topics

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Jul 21 01:20PM -0400  

    Hello Miriam,
     
    The files located on our test server (
    http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/liftOver/) have not yet
    been reviewed by our quality assurance team. You are welcome to use these
    files, however, please keep in mind our test server contains a lot of
    experimental data and may undergo changes.
     
    If you have any further questions, please reply to genome <at> 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
    genome-www <at> soe.ucsc.edu.
     
    - - -
    Luvina Guruvadoo
    UCSC Genome Bioinformatics Group
     
     
     
    On Sun, Jul 20, 2014 at 7:54 PM, Miriam Huntley <mhuntley <at> fas.harvard.edu>
    wrote:
     

     

    meharji arumilli <mehar.com <at> gmail.com> Jul 21 07:09PM +0300  

    Hi,
     
     
    I tried using the following scripts to convert bed file to GTF file which
    are available at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
     
    *bedToGenePred input.bed stdout | genePredToGtf -utr file stdin output.gtf*
     
    I have used the genePredToGtf script with -utr option to add 5UTR and 3UTR
    features. However, the output doesn't have the UTR features in the final
    GTF file irrespective of -utr option.
     
    Could it be a bug in the script? Could someone give any ideas/suggestions
    to achieve this.
     
     
    --
    Best Regards
    Mehar

     

    "Igor Mett" <imett <at> quarkpharma.com> Jul 20 11:04AM +0300  

    Dear Sir or Madame,

    I have got some predicted miRNA sites within my gene of interest in USCS
    Genome Browser.

    What does it mean: Highly conserved miRNA families?

    Have I understood right that the predicted sites are conserved among
    same gene of multiple vertebrates?

    Thanks in advance,

    Sincerely yours,

     
    Igor Mett
     
    Senior Scientist
     
    Quark Pharmaceuticals Inc./QBI Enterprises Ltd.
     

     
    QBI Enterprises Ltd.
     
    Nes Ziona ISRAEL
     
    Tel: +972 8 9305232
     
    Fax +972 8 9406476
     
    imett <at> quarkpharma.com <mailto:AAbramoff <at> quarkpharma.com>
     
    www.quarkpharma.com <http://www.quarkpharma.com/>
     

     

     
    The material in this transmission may contain confidential and/or
    proprietary information intended only for the addressee. If you are not
    the addressee, any disclosure or use of this information by you is
    strictly prohibited. If you have received this transmission in error,
    please delete it, destroy all copies, and notify Quark Pharmaceuticals /
    QBI Enterprises by telephone or by return email. Thank you.

     

    "Rege, Mayuri" <Mayuri.Rege <at> umassmed.edu> Jul 19 11:37PM  

    I am having trouble viewing a bedGraph file in the Genome browser depending on the genome assembly version I use.
    The older assembly (sacCer1) of the yeast genome is the only one that I can view the track with.
    The error I get with the newer assemblies (sacCer2 and sacCer3) is Error Unrecognized format type=bedGraph line 2 of custom track
     
    Here is the start file:
    track type=bedGraph name=Histone
    chr1 11604 11896 1.49203
     
    The release log<https://genome.ucsc.edu/goldenPath/releaseLog.html> from UCSC lists all three assemblies as available. How can this be fixed? Thank you!
     
    -M Rege
    Graduate student
    University of Massachusetts Medical School
    Worcester, MA

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 19 Jul 19:15 2014

Digest for genome <at> soe.ucsc.edu - 1 update in 1 topic

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Matthew Speir <mspeir <at> soe.ucsc.edu> Jul 18 02:37PM -0700  

    Hi Kipper,
     
    Thank you for your question about using hgWiggle. We have been unable to
    reproduce the error on our end. Are you still experiencing issues using
    hgWiggle with a local wib file?
     
    If you have any further questions, please reply to genome <at> 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 genome-www <at> soe.ucsc.edu.
     
    Matthew Speir
    UCSC Genome Bioinformatics Group
     
     
    On 7/3/14, 3:42 AM, Kipper Fletez-Brant wrote:

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 12 Jul 19:11 2014

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Matthew Speir <mspeir <at> soe.ucsc.edu> Jul 11 03:45PM -0700  

    Hi Safiye,
     
    Thank you for your question about Table Browser output for the Poly(A)
    track. Could you please clarify what you would like your output to look
    like? Knowing this will help us recommend some settings to get you the
    output you want.
     
    I hope this is helpful. If you have any further questions, please reply
    to genome <at> 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 genome-www <at> soe.ucsc.edu.
     
    Matthew Speir
    UCSC Genome Bioinformatics Group
     
     
    On 7/3/14, 2:26 PM, Safiye Özkan wrote:

     

    Brian Lee <brianlee <at> soe.ucsc.edu> Jul 11 10:35AM -0700  

    Dear Holly,
     
    Thank you for using the UCSC Genome Browser and your question about ENCODE
    data.
     
    You are correct that the 'origAssembly=hg18', means the data was originally
    produced for hg18, but has now been lifted over to hg19 (so they are hg19
    coordinates).
     
    For the original production files from Broad Histone, you can select the
    Antibody Target to "H3K27me3 (07-449)" to find 150 files,
    http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHistone, but
    I missing the mention of Stanford or UCDavis, so it is unclear where that
    connection is coming from in your question. If you scroll down to the
    bottom of the page you can read a track description and method sections,
    which may help answer questions. If you wish to contact the lab producing
    data when you can't find the answer, please look to the credits section and
    inquire directly to the contact listed.
     
    Please know if you are going to compare data between different labs,
    instead of beginning with files from the original production groups, please
    look to the analysis group where files were uniformly processed enabling
    better comparisons. This will likely answer your question regarding which
    data to us. Here you can see the external analysis hub's Histone page:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hub_4607_uniformHistone&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt
     
    Here is a link to the external files for the analysis histone files (note
    the uniformHistone.html file displays in the above page link provided to
    load this externally hosted hub):
    http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/
     
    Thank you again for your inquiry and using the UCSC Genome Browser. If you
    have any further questions, please reply to genome <at> 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
    genome-www <at> soe.ucsc.edu.
     
    All the best,
     
    Brian Lee
    UCSC Genome Bioinformatics Group
     
     

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 10 Jul 19:18 2014

Digest for genome <at> soe.ucsc.edu - 3 updates in 2 topics

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Tongyao Wang <wang.to <at> husky.neu.edu> Jul 09 09:03PM -0400  

    Hello,
     
    I am using mysql commands to connect UCSC database to do some
    bioinformatics analysis. But I cannot locate the unique gene ID, like 2838
    for GPR15. I am sure UCSC has it, because I tried to search by the ID in
    UCSC browser. Do you mind to tell me which table has that column? Thanks.
     
    Best,
    Tongyao
     
    --
    Tongyao Wang
    Bioinformatics
    College of Science
    Northeastern University
    wang.to <at> husky.neu.edu
    860-617-0735

     

    "Steve Heitner" <steve <at> soe.ucsc.edu> Jul 09 10:17AM -0700  

    Hello, Rippei.
     
    Could you please provide some clarification on where you are attempting to
    remove hubs from? Are you using the Browser and you no longer want to
    display hubs that you have selected? Are you using a session and no longer
    want the hubs to appear in your session? Are you using the Browser and you
    don't want to see specific hubs displayed in the list of public hubs? Are
    you running a mirror site and would like to remove specific hubs from the
    list of public hubs?
     
    Please contact us again at genome <at> 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 genome-www <at> soe.ucsc.edu.
     
    ---
    Steve Heitner
    UCSC Genome Bioinformatics Group
     

     
    From: Hayashi,Rippei [mailto:rippei.hayashi <at> imba.oeaw.ac.at]
    Sent: Wednesday, July 09, 2014 3:13 AM
    To: genome <at> soe.ucsc.edu
    Subject: [genome] deleting the old hubs
     

     
    Dear my colleague,
     

     
    I would like to remove the hubs that are no longer useful, but am wondering
    how to do it.
     
    Would you let me know how to do it?
     

     
    Many thanks
     
    Rippei in Austria
     

     
    --

     

    "Steve Heitner" <steve <at> soe.ucsc.edu> Jul 09 11:05AM -0700  

    Hello, Rippei.
     
    Based on the screen shot you sent, it appears related to a bug that we
    recently fixed. The fix will not be available on our public site until our
    next release which is scheduled for Tuesday July 29. In the meantime, you
    can clear all hubs by performing a cart reset at
    http://genome.ucsc.edu/cgi-bin/cartReset. Please be aware that this will
    reset all of your Browser settings back to the default.
     
    Please contact us again at genome <at> 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 genome-www <at> soe.ucsc.edu.
     
    ---
    Steve Heitner
    UCSC Genome Bioinformatics Group
     

     
    From: Hayashi,Rippei [mailto:rippei.hayashi <at> imba.oeaw.ac.at]
    Sent: Wednesday, July 09, 2014 10:38 AM
    To: steve <at> soe.ucsc.edu
    Subject: Re: [genome] deleting the old hubs
     

     
    Dear Steve
     

     
    Thank you for your prompt reply.
     
    I would like to remove track data hubs that I once imported yet I not longer
    need.
     
    Somehow I can not select the "disconnection" cartoon for the hubs that I
    imported a while ago and some of them keep showing error messages.
     
    (Please find the attached snapshot. I wanted to attach this image in my
    initial email, but it was disallowed due to the size limit of the email.
    Hope it works this time.)
     

     
    I basically would like to clear up all hubs and start the page from scratch.
     

     
    Thanks again for your help.
     
    Rippei
     

     

     
    From: Steve Heitner <steve <at> soe.ucsc.edu>
    Reply-To: "steve <at> soe.ucsc.edu" <steve <at> soe.ucsc.edu>
    Date: Wednesday, July 9, 2014 7:17 PM
    To: IT Services <rippei.hayashi <at> imba.oeaw.ac.at>, "genome <at> soe.ucsc.edu"
    <genome <at> soe.ucsc.edu>
    Subject: RE: [genome] deleting the old hubs
     

     
    Hello, Rippei.
     
    Could you please provide some clarification on where you are attempting to
    remove hubs from? Are you using the Browser and you no longer want to
    display hubs that you have selected? Are you using a session and no longer
    want the hubs to appear in your session? Are you using the Browser and you
    don't want to see specific hubs displayed in the list of public hubs? Are
    you running a mirror site and would like to remove specific hubs from the
    list of public hubs?
     
    Please contact us again at genome <at> 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 genome-www <at> soe.ucsc.edu.
     
    ---
    Steve Heitner
    UCSC Genome Bioinformatics Group
     

     
    From: Hayashi,Rippei [mailto:rippei.hayashi <at> imba.oeaw.ac.at]
    Sent: Wednesday, July 09, 2014 3:13 AM
    To: genome <at> soe.ucsc.edu
    Subject: [genome] deleting the old hubs
     

     
    Dear my colleague,
     

     
    I would like to remove the hubs that are no longer useful, but am wondering
    how to do it.
     
    Would you let me know how to do it?
     

     
    Many thanks
     
    Rippei in Austria
     

     
    --

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 8 Jul 19:07 2014

Digest for genome <at> soe.ucsc.edu - 3 updates in 3 topics

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Jul 07 03:08PM -0700  

    Hello Joseph,
     
    Thanks for your question, but I was unable to locate these tracks on our
    main site (http://genome.ucsc.edu). Are you viewing these tracks on a
    mirror site such as https://cgwb.nci.nih.gov/cgi-bin/hgTracks? If so, we
    suggest you contact the folks at the CBIIT/National Cancer Institute who
    maintain that site.
     
    If you have any further questions, please reply to genome <at> 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
    genome-www <at> soe.ucsc.edu.
     
    - - -
    Luvina Guruvadoo
    UCSC Genome Bioinformatics Group
     
     
     

     

    Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Jul 07 01:13PM -0700  

    Hello Khosrow,
     
    Thank you for your question. You should be able to extract the non-coding
    regions on chr Y using the Table Browser. To do this, navigate to
    http://genome.ucsc.edu/cgi-bin/hgTables and make the following selections
    (for this example, I'm using the RefSeq Genes track):
     
    Clade: Mammal
    Genome: Human
    Assembly: Feb. 2009 (GRCh37/hg19)
    Group: Genes and Gene Prediction Tracks
    Track: RefSeq Genes
    Table: refGene
    Region: chrY
     
    Click on 'filter' and enter the following in the "Free-form query" box:
    cdsStart=cdsEnd. Click the "submit" button, followed by "get output". Leave
    "genomic" selected and click "submit". Configure the sequence display as
    desired and click the "get output" button.
     
    If you have any further questions, please reply to genome <at> 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
    genome-www <at> soe.ucsc.edu.
     
    - - -
    Luvina Guruvadoo
    UCSC Genome Bioinformatics Group
     
     
     

     

    Jonathan Casper <jcasper <at> soe.ucsc.edu> Jul 07 11:17AM -0700  

    Hello Steffen,
     
    Thank you for your question about using the right-click menu with IE 10 on
    Windows 7. We are unable to reproduce your issue here. Are there additional
    details you can give us about installed plugins or anything else particular
    to your computer? Please note that the UCSC Genome Browser does require
    javascript to function properly. If the update to your computer adjusted
    your security settings, IE 10 might now be blocking the scripts that create
    the right-click menu. Those settings would not also be applied to Mozilla
    Firefox, explaining why our site continues to work for you in that browser.
     
    I hope this is helpful. If you have any further questions, please reply to
    genome <at> soe.ucsc.edu or genome-mirror <at> 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 genome-www <at> soe.ucsc.edu.
     
    --
    Jonathan Casper
    UCSC Genome Bioinformatics Group
     
     
    On Fri, Jul 4, 2014 at 4:36 AM, Koppsieker, Steffen <

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 2 Jul 19:19 2014

Digest for genome <at> soe.ucsc.edu - 1 update in 1 topic

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Kipper Fletez-Brant <cafletezbrant <at> gmail.com> Jul 02 09:26AM -0400  

    I'm writing this so that anyone else having the same problem that I had
    can get up to speed.
     
    If you find yourself having gone through all of the steps in the set of
    quoted emails and things still don't work, add the following 2 lines to
    your .hg.conf:
     
    gbdbLoc1=/path/to/relevant/WIB/file/
    gbdbLoc2=http://hgdownload.cse.ucsc.edu/gbdb/
     
    This seemed to fix it for me (I discovered this by grepping the kent src
    tree files for mention of the /gbdb/ directory and discovered the file
    ex.hg.conf, which explained in great detail many other possible settings)
     
    On 07/01/2014 09:26 AM, Kipper Fletez-Brant wrote:

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 23 Jun 19:13 2014

Digest for genome <at> soe.ucsc.edu - 4 updates in 4 topics

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Shawn Burgess <burgess <at> mail.nih.gov> Jun 23 12:43PM -0400  

    Hi:
     
    I was wondering if I could get a decision on this question. We are submitting the revised manuscript today and would like to include the fact that it is registered with UCSC if that is the case.
     
    Thanks,
    S
     
     
    Begin forwarded message:
     

     

    Daofeng Li <lidaof <at> gmail.com> Jun 23 10:24AM -0500  

    Hi Matthew,
     
    This was very useful, thank you so much.
     
    Daofeng
     
     

     

    Kausik Ganguly <kausikganguly6 <at> gmail.com> Jun 23 06:59PM +0530  

    SIr, how can we use UCSC genome browser and ENCODE project related tools to
    find out Single Nucleotide Polymorphisms (SNPs) that are residing within a
    particular Genomic co-ordinate range, which is shown to be regulatory from
    the *"Regulatory Elements Database" *(Sheffield NC, Thurman RE, Song L,
    Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS. Patterns
    of regulatory activity across diverse human cell types predict tissue
    identity, transcription factor binding, and long-range interactions
    <http://www.ncbi.nlm.nih.gov/pubmed/23482648>. *Genome Res*. 2013
    May;23(5):777-88. PMID: 23482648; PMCID: PMC3638134)?
     
    For example when we searched for *BRCA1* gene in *Regulatory Elements
    Database*, we got *Top 10 Correlated DHS sites*, under which we searched
    the region >
     
    LocationCluster P-valuechr17:41132840-41132990
    <http://dnase.genome.duke.edu/dhsDetail.php?dhsID=1106270> 333
    <http://dnase.genome.duke.edu/clusterDetail.php?clusterID=333> 0.001
    Now, we wish to know if there is any SNP within the range
    chr17:41132840-41132990
    <http://dnase.genome.duke.edu/dhsDetail.php?dhsID=1106270>, using UCSC
    genome browser tool.
     
    We will be highly obliged with your kind co-operation;
     
    Kausik Ganguly,
    Research Fellow,
    Dept. of Genetics,
    Dr. Mainak Sengupta's Lab,
    University of Calcutta.

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 16 Jun 19:12 2014

Digest for genome <at> soe.ucsc.edu - 4 updates in 4 topics

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Harold Pimentel <haroldpimentel <at> gmail.com> Jun 15 07:52PM -0700  

    Hi all,
     
    I have some bigWig coverage files made from bed graph files (which were
    made from genomeCoverageBed on some BAM files) and I'm trying to view them
    on the genome browser. The original data was mapped to the Ensembl version
    of the human genome. Interestingly, the reads show up correctly on a
    browser track even though the chromosome names do not match in the BAM
    files (i.e. 1 vs chr1). Unfortunately, the same is not true for the bigWig
    files and the track displays completely empty on the genome browser. Is
    there something I can change on the browser to properly display this track?
     
    If not, is there an easy way to convert the chromosome names on the bigWig
    file to match the genome browser?
     
     
     
    Thanks!
     
    Harold

     

    "Trakhtenberg, Feliks" <Ephraim.Trakhtenberg <at> childrens.harvard.edu> Jun 15 07:51PM  

    Hello,
     
     
     
    I would appreciate if you could please email me a link for downloading the latest mouse transcripts GTF file, and answer the following questions:
     
    (1) Does the GTF include not-redundant transcripts from RefSeq, GenBank, and Ensembl?
     
    (2) Does GTF include UCSC transcripts not found in the above databases?
     
    (3) Are there other databases from which transcripts are added to the GTF?
     
    (4) Are miRNAs, piRNAs, and all other species of non-coding RNA included in the GTF?
     
     
     
    Thank you,
     
    Ephraim Trakhtenberg, Ph.D.
     
     
     
    Postdoctoral Research Fellow
     
    Boston Children's Hospital, HMS
     
    Neurosurgery Dept. Benowitz lab
    Center for Life Science, Room 13-071
    3 Blackfan Circle. Boston, MA 02115
     
    Tel:305-606-7079<tel:305-606-7079>

     

    Pete Shepard <peter.shepard <at> gmail.com> Jun 15 06:15AM -0700  

    Dear UCSC Genome Browser,
     
    I have a list of gene symbols or gene identifiers of some sort, I would
    like to obtain refseq IDs for each symbol/gene identifier. Using my current
    approach, I can find a refseq IDs for >95% of the gene symbols.
     
    For the remaining 5%, I paste the gene symbol into the Genome Browser's
    search term and this almost always get me the output I want.
     
    My question is, can I to create a table using the Table Browser that can
    reproduce what
    the search term feature in the Genome Browser is doing?
     
    Thank you

     

    Fei Chen <feichen316 <at> gmail.com> Jun 13 10:07PM -0700  

    Hi,
     
    I have problem to upload the newest C.elegans genome WS242. It seemed that
    the GFF2 or GFF3 files I downloaded from wormbase could not be recognized
    by UCSC genome browser. Can you help?
     
    Best,
    Fei

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 14 Jun 19:14 2014

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Jonathan Casper <jcasper <at> soe.ucsc.edu> Jun 13 01:21PM -0700  

    Hello Igor,
     
    Thank you for your question about an update to the C. elegans genome on the
    UCSC Genome Browser. Our funding mandates that we focus on vertebrate
    genomes, so we have been unable to pursue an update to C. elegans. You are
    welcome to create an assembly hub, however, as noted in this mailing list
    question:
    https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/eZ_wBLH66I0/discussion.
    Assembly hubs are a tool we recently developed to allow users to display
    their own genome assemblies and accompanying annotation in the UCSC Genome
    Browser.
     
    For more information on creating assembly hubs, please review the track hub
    help pages at http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html and
    the assembly hubs wiki page at
    http://genomewiki.ucsc.edu/index.php/Assembly_Hubs.
     
    I hope this is helpful. If you have any further questions, please reply to
    genome <at> soe.ucsc.edu or genome-mirror <at> 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 genome-www <at> soe.ucsc.edu.
     
    --
    Jonathan Casper
    UCSC Genome Bioinformatics Group
     
     
    On Fri, Jun 13, 2014 at 7:55 AM, Dolgalev, Igor <Igor.Dolgalev <at> nyumc.org>
    wrote:
     

     

    "Steve Heitner" <steve <at> soe.ucsc.edu> Jun 13 12:09PM -0700  

    Hello, Bob.
     
    I just looked up a SNP ID at dbSNP and the coordinates appear to be in terms
    of GRCh38. Patches to GRCh37 exist outside of GRCh37, so GRCh37 coordinates
    should be identical regardless of patch version.
     
    That being said, we do have a liftOver utility to convert GRCh38 (hg38)
    coordinates to GRCh37 (hg19) coordinates at
    http://genome.ucsc.edu/cgi-bin/hgLiftOver. The web utility is free for all
    to use. We also have a downloadable standalone liftOver utility at
    http://hgdownload.cse.ucsc.edu/downloads.html#utilities_downloads. This is
    free for academic, non-commercial and personal use, but would require the
    purchase of a license for commercial use. Please see
    http://genome.ucsc.edu/license/ for further information.
     
    Please contact us again at genome <at> 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 genome-www <at> soe.ucsc.edu.
     
    ---
    Steve Heitner
    UCSC Genome Bioinformatics Group
     

     
    From: Bob [mailto:rrooney <at> genome-explorations.com]
    Sent: Thursday, June 12, 2014 9:08 AM
    To: genome <at> soe.ucsc.edu
    Subject: [genome] Conversion of UCSC genome coordinates to those in NCBI
     

     
    Hi,
     

     
    Currently, NCBI and dbSNP only show genomic coordinates for GRCh38 and
    GRCh37.p13. There are substantial differences between GRCH37.p13 (and, of
    course, GRCh38) and the GRCh37 (Feb2009) build that you are using. Because
    two other utilities I am using (Affymetrix DMET and Ampliseq Designer for
    Ion PGM) are based on the GRCh37 (Feb2009) build and refer to your site, is
    there a convenient way to convert genomic coordinates for new SNPs in dbSNP
    to this older build? I would like to do this in batch format, as I have a
    large number of SNPs to convert.
     

     
    Best regards,
     
    Bob Rooney
     
    Robert J. Rooney, PhD
    Scientific Director/CSO
    Genome Explorations Inc.
    654 Jefferson Ave.
    Memphis, TN 38105 USA
    Tel: 901-405-4400
    Fax: 901-578-5709
    email: rrooney <at> genome-explorations.com
    web: www.genome-explorations.com
     
     
    CONFIDENTIALITY NOTICE: This communication and any attachments may contain
    confidential and privileged information for the use of the designated
    recipient(s) named above. Distribution, reproduction or any other use of
    this transmission by any party other than the intended recipient(s) is
    prohibited.
     
    --

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 7 Jun 19:06 2014

Digest for genome <at> soe.ucsc.edu - 4 updates in 1 topic

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Hiram Clawson <hiram <at> soe.ucsc.edu> Jun 06 06:51PM -0700  

    I don't see the requirement for any quoting of table names:
    http://dev.mysql.com/doc/refman/5.6/en/create-table.html
     
    > database, assuming that the database exists. If you use quoted identifiers,
    > quote the database and table names separately. For example,
    > write `mydb`.`mytbl`, not `mydb.mytbl`.
     
    The quotes appear to be optional. Probably required for unusual characters
    in the names.
     
    We have no code in the genome browser that adds quotes around
    the table names. I guess we have always been within our expected
    character set.
     
    HOWEVER, this doesn't explain this current situation. Your name appears
    to be perfectly ordinary. I see no unusual characters in the name.
    I am very curious what it is that MySQL is objecting to in this seemingly
    ordinary name.
     
    On 6/6/14 6:43 PM, Andrey Kartashov wrote:

     

    Hiram Clawson <hiram <at> soe.ucsc.edu> Jun 06 07:22PM -0700  

    I still need to figure out what is going on. There is nothing
    wrong with the name of this table according to the MySQL doc or
    the browser software. It should be working, I need to find out
    why it is not. I have full debugging MySQL source available here
    and can find out in that source what it is complaining about.
     
    --Hiram
     
    On 6/6/14 7:15 PM, Andrey Kartashov wrote:

     

    Hiram Clawson <hiram <at> soe.ucsc.edu> Jun 06 11:09PM -0700  

    Good Evening Andrey:
     
    It may be happen that the name beginning 278E986 could be interpreted
    as a number by MySQL. That would be a problem since numbers are
    illegal as names without 'protection' quotes. If this is true, then
    a work-around would be to insure your generated names always begin
    with a letter instead of numbers.
     
    You may have found one place in the browser code which makes this particular
    example work. However, for the general case, this would be a major
    overhaul of the browser code to quote all names in all cases throughout
    the source tree. And if the code did allow any arbitrary name with
    quotes, this would cause down-stream processing difficulties for any
    data consumers of ours as surely unusual character codes would begin
    to infect the data stream. That doesn't sound like a good way to go.
    I'm sure this issue will prompt much discussion at our next engineering
    meeting.
     
    --Hiram
     
    http://etutorials.org/SQL/MySQL/Part+I+General+MySQL+Use/Chapter+3.+MySQL+SQL+Syntax+and+Use/MySQL+Naming+Rules/
     
    On 6/6/14 10:06 PM, Andrey Kartashov wrote:

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.
genome | 4 Jun 19:26 2014

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

    Brian Lee <brianlee <at> soe.ucsc.edu> Jun 03 01:50PM -0700  

    Dear David,
     
    Thank you for using the UCSC Genome Browser and for endeavoring to load
    dynamic track hubs. An engineer will contact you directly to discuss
    possible approaches to implementing a temporary status of your hubs to
    avoid the stacking up of displays.
     
    Thank you again for contacting us and using the UCSC Genome Browser. If you
    have any further unrelated questions, please reply to genome <at> 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
    genome-www <at> soe.ucsc.edu.
     
    All the best,
    Brian Lee
    UCSC Genome Bioinformatics Group
     
     
    On Tue, Jun 3, 2014 at 9:20 AM, David Bujold <david.bujold <at> mail.mcgill.ca>
    wrote:
     

     

    Jonathan Casper <jcasper <at> soe.ucsc.edu> Jun 03 11:00AM -0700  

    Hello Ivan,
     
    Thank you for your question about obtaining BLAT binaries with fewer
    dynamically linked libraries. Our engineers tell me that they will see what
    they can do about reducing the number of these dependencies. Ideally we'd
    like to remove as many as we possibly can, but I do not have a timetable
    for when an upgraded version will be ready.
     
    I hope this is helpful. If you have any further questions, please reply to
    genome <at> soe.ucsc.edu or genome-mirror <at> 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 genome-www <at> soe.ucsc.edu.
     
    --
    Jonathan Casper
    UCSC Genome Bioinformatics Group
     
     
    On Thu, May 29, 2014 at 6:11 PM, Ivan Adzhubey <

     

To unsubscribe from this group and stop receiving emails from it, send an email to genome+unsubscribe <at> soe.ucsc.edu.

Gmane