genome | 20 Sep 19:07 2014

Digest for genome <at> soe.ucsc.edu - 7 updates in 4 topics

<M.S.Roost <at> lumc.nl>: Sep 19 05:44PM

Dear Sir or Madam,
 
I'm trying to fetch genomic data from UCSC via R (Biomart), and I've been having problems getting it for a few hours now. Could it be there is some maintenance going on?
 
Thank you very much!
 
Best Regards,
Matthias
Matthew Speir <mspeir <at> soe.ucsc.edu>: Sep 19 04:01PM -0700

Hi Matthias,
 
Thank you for your question about the UCSC Genome Browser. We are not
doing any maintenance on our public MySQL server, nor am I aware of any
issues with this server. Are you still experiencing issues at this time?
 
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
 
 
Matthew Speir <mspeir <at> soe.ucsc.edu>: Sep 19 03:53PM -0700

Hi Pengyao,
 
Thank you for your question about gene track updates for the dm3
assembly. There are two gene tracks on the dm3 assembly that are updated
on a regular basis. The RefSeq Genes track is update with new
information that we download from RefSeq on a nightly basis. The data
for the RefSeq Genes track was last updated 2014-09-13. The Ensembl
Genes track is updated whenever Ensembl releases a new version of their
gene predictions for the dm3 assembly. The data for the Ensembl Genes
track was last updated 2014-03-11. You can always see when the data in a
track was last updated by looking at a track's description page. You can
get to a track's description page by clicking the track name in the
groups below the main browser display, or by clicking the grey bar next
to the track on the far left of the main browser display. For example,
on the dm3 RefSeq Genes description page,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm3&g=refGene, you can see
the date just below the track settings on the line labeled "Data last
updated".
 
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 9/18/14, 12:07 PM, Pengyao Jiang wrote:
Matthew Speir <mspeir <at> soe.ucsc.edu>: Sep 19 11:16AM -0700

Hi Nelson,
 
Thank you for your question about updating the D. melanogaster assembly
in the UCSC Genome Browser. A preview of the BDGP Release 6/dm6 Genome
Browser is available on our preview site at
http://genome-preview.ucsc.edu/cgi-bin/hgGateway?db=dm6. However, please
keep in mind that this our test server, and that much of the data has
not undergone our standard quality review process and is subject to
change. We do have plans to release this to our public website at
http://genome.ucsc.edu/, but I do not have a projected date of when that
might happen.
 
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 9/18/14, 8:15 PM, Nelson Lau wrote:
Nelson Lau <nlau <at> brandeis.edu>: Sep 19 02:41PM -0400

Thanks, Matthew. Is the Liftover tool able to help us convert the
Dm3/Release5 coordinates to the Dm6/Release6 coordinates? We have a paper
accepted where the work was done on Dm3, but the journal would prefer all
the coordinates be adjusted to Dm6, including BED files. I understand this
build is on the test server, but presumably the new build will be released
soon? Please advise how we can convert all our file coordinates to Dm6.
 
 
 
*From:* Matthew Speir [mailto:mspeir <at> soe.ucsc.edu]
*Sent:* Friday, September 19, 2014 2:16 PM
*To:* Nelson Lau; genome <at> soe.ucsc.edu
*Subject:* Re: [genome] Release 6 Drosophila melanogaster genome?
 
 
 
Hi Nelson,
 
Thank you for your question about updating the D. melanogaster assembly in
the UCSC Genome Browser. A preview of the BDGP Release 6/dm6 Genome Browser
is available on our preview site at
http://genome-preview.ucsc.edu/cgi-bin/hgGateway?db=dm6. However, please
keep in mind that this our test server, and that much of the data has not
undergone our standard quality review process and is subject to change. We
do have plans to release this to our public website at
http://genome.ucsc.edu/, but I do not have a projected date of when that
might happen.
 
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 9/18/14, 8:15 PM, Nelson Lau wrote:
 
Hello,
 
 
 
Do you have an ETA when the newest Release 6 of the Drosophila Melanogaster
genome will be loaded into the UCSC Browser? The current latest build is
Dm3, Release 5.
 
 
 
Thanks,
 
 
 
Nelson Lau, Ph.D.
 
Assistant Professor - Biology
 
Brandeis University
 
415 South St, MS029
 
Science Receiving
 
Waltham MA 02454, USA
 
Ph: 781-736-2445
http://www.bio.brandeis.edu/laulab
 
 
 
 
 
--
Matthew Speir <mspeir <at> soe.ucsc.edu>: Sep 19 01:54PM -0700

Hi Nelson,
 
Yes, you can use the liftOver tool just like you normally would to
convert dm3 to dm6 coordinates. You can access the web interface for
liftOver on our preview site at
http://genome-preview.ucsc.edu/cgi-bin/hgLiftOver. To convert the
coordinates from dm3 to dm6 use the following settings:
 
Original Genome: D. melanogaster
Original Assembly: BDGP R5
New Genome: D. melanogaster
New Assembly: BDGP Release 6 + ISO1 MT
 
If you want to use the command line liftOver utility, you can find the
liftOver chain file on our preview downloads server here:
http://hgdownload-test.soe.ucsc.edu/goldenPath/dm3/liftOver/dm3ToDm6.over.chain.gz.
Again, please keep in mind that the data on our preview servers has yet
to undergo our standard quality assurance process and may be subject to
change.
 
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 9/19/14, 11:41 AM, Nelson Lau wrote:
Jonathan Casper <jcasper <at> soe.ucsc.edu>: Sep 19 12:20PM -0700

Hello Nitika,
 
Thank you for your question about finding genes that match your probe sets.
I suggest that you start by building a custom track from your probe sets
and then use the "intersection" part of the UCSC Table Browser (
http://genome.ucsc.edu/cgi-bin/hgTables) to get the genes that overlap with
your probe sets. See
http://genome.ucsc.edu/goldenPath/help/customTrack.html for
more information about building a custom track, and
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection for
more information on using intersections in the Table Browser.
 
Depending on what gene information you need, the intersection tool might
not be enough for your research. If that is the case, the tools at Galaxy (
https://usegalaxy.org) can help you to get more specific gene information.
The following mailing list questions describe how to use the Table Browser
together with the tools at Galaxy to find gene information:
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/LdYxhGwswno/discussion
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/lF0UpVKYi8I/discussion
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/y7zQDKO-8Hk/discussion
 
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
 
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genome | 13 Sep 19:05 2014

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

Matthew Speir <mspeir <at> soe.ucsc.edu>: Sep 12 03:41PM -0700

Hi Bill,
 
Thank you for your question about getting gene symbols as part of your
from the Table Browser. You are on the right track with your current
Table Browser settings, and the only issue is your output settings. The
reason you are not getting gene symbols as part of your output is
because these are not stored in the knownGene table for the UCSC Genes
track, but instead stored in a linked table. When you select the output
option "all fields from selected table", you are only getting the
information contained in the knownGene table. I recommend using the
"selected fields from primary and related tables" output option. After
you click "get output", you will be taken to another page where you will
be able to select fields from both the knownGene table and various
linked tables that you want as part of your output. On this page, select
those fields from the "Select Fields from hg19.knownGene" section that
you are interested in. In the "hg19.kgXref fields" section, you will
find a number of alternative IDs for the transcripts in the knownGene
table. Check the box next to "geneSymbol", and any other IDs you are
interested in. Finally, click "get output". Your output will consist of
the fields you selected as columns in order starting from the top of the
"hg19.knownGene" section. While this output option doesn't necessarily
format your output in a terribly useful way, you can use a simple UNIX
command line utility such as awk to rearrange the columns however 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 9/11/14, 7:54 AM, LaFramboise, William A wrote:
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Sep 12 02:45PM -0700

Hello Peter,
 
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 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.
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 Fri, Sep 12, 2014 at 1:07 AM, Peter Frommolt <peter.frommolt <at> uni-koeln.de
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Sep 12 12:56PM -0700

Hello,
 
Thanks for your question. I'm assuming you used the Human mRNAs track on
hg19 to download the sequence:
http://genome.ucsc.edu/cgi-bin/hgc?db=hg19&g=mrna&i=AY590150. This track is
generated by aligning GenBank human mRNAs against the genome using BLAT. It
appears PIF (proteolysis inducing factor) has not yet been annotated in the
mouse reference assembly, see http://www.ncbi.nlm.nih.gov/gene/100126829.
 
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
 
 
Brian Lee <brianlee <at> soe.ucsc.edu>: Sep 12 12:16PM -0700

Dear Hai-Bing Xie,
 
Thank you for using the UCSC Genome Browser and your question about the
chromosomal coordinates for Factorbook-identified canonical motifs seen as
green highlighted bars in the clustered transcription factor binding sites
track.
 
The Factorbook motif identifications and localizations where provided by
the Zlab (http://zlab.umassmed.edu/zlab/) at the UMass Medical School and
are available in two tables, the first providing the position of each
factorbook item, factorbookMotifPos, the second providing the position
weight matrix, factorbookMotifPwm.
 
These are located in the general hg19 annotation database section of our
hgdownload server along with a corresponding .sql file:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/factorbookMotifPos.txt.gz
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/factorbookMotifPwm.txt.gz
 
You can access these table via the Public MySQL server:
http://genome.ucsc.edu/goldenPath/help/mysql.html
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e 'show tables
like "factorbook%";' hg19
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e 'select * from
factorbookMotifPos;' hg19
 
There are two additional tables, factorbookMotifCanonical and
factorbookGeneAlias, that help map the information from the Zlab to the
target terms used in the UCSC Genome Browser.
 
You can alternatively use the hg19 Table Browser to access these tables:
http://genome.ucsc.edu/cgi-bin/hgTables
1. Set the "group:" to "All tables"
2. Set the table to "factorbookMotifPos"
3. Click "genome" to get the entire table, or click the "define regions"
button and get enter coordinates of interest, such as "chrX 14000000
150000000".
4. Click "get output". If desired, you could set "output format" to "custom
track" and see the results in the browser.
 
What is displayed in the wgEncodeRegTfbsClustered track is the result of a
computational mapping of the factorbookMotifPos items to the clustered TFBS
locations filtered for the highest score per cluster. There is not an easy
path to obtain these exact mappings, but you can perform similar operations
with the Table Browser.
 
For example if you were looking at the region around SOD1,
chr21:33,031,597-33,041,570, you could enter this as the defined region in
the Table Browser (step 3).
4. Click the "create" button next to "filter".
5. Set the "score" is ">" then a desired amount, such as "2" and click
"submit".
6. Click the "create" button next to "intersection".
7. Select "group: Regulation" and "track: Txn Factor ChIP" and "table:
wgEncodeRegTfbsClusteredV3" then click "submit".
8. Click "get output". If desired, you could set "output format" to "custom
track" and see the results in the browser.
 
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
 
 
Matthew Speir <mspeir <at> soe.ucsc.edu>: Sep 12 10:35AM -0700

Hi Turgay,
 
Thank you for your questions about the UCSC Genome Browser. You are
correct about the coordinate systems used in our tables, and
subsequently in the files you downloaded. In our tables, we use 0-based
start coordinates and 1-based end coordinates. You can read more this on
the following pages:
 
* http://genome.ucsc.edu/FAQ/FAQtracks#tracks1
* http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
 
 
By default, the Genome Browser displays the sequence of the plus strand.
The NBPF1 gene, however, is on the minus strand. When you were looking
at this position in the Browser, it is likely that you were looking at
the sequence for this codon on the plus strand, which is "AGA". If you
were to view this on the minus strand, you would see that the sequence
for this codon is "UCU", which does in fact code for serine. Please see
this answer to a previous mailing list question for a great explanation
of our strand display for genes and how to view the minus strand in the
Browser:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/_EjI7ddU_PY/O9UB7DwBvc8J.
 
 
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 9/11/14, 8:40 AM, Turgay Aytac wrote:
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genome | 6 Sep 19:15 2014

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

Jonathan Casper <jcasper <at> soe.ucsc.edu>: Sep 05 11:11AM -0700

Hello Alireza,
 
You are absolutely right. When looking at a chain file, the coordinates for
things on the - strand are changed around. To find the item on the +
strand, you will need to use the coordinates (tSize-tEnd, tSize-tStart].
When using a GTF file, you do not need to change the coordinates for items
on the - strand.
 
It is unfortunate that differences like this exist, which can be confusing
for people who need to work with many file formats. That is part of why we
try to provide tools for working with these file formats and converting
between them, so that these differences are hidden away.
 
A word of warning: you may also need to work with the PSL data format (
http://genome.ucsc.edu/FAQ/FAQformat.html#format2) at some point. PSL has
its own way of describing items on the - strand. The start and stop
position for each alignment use + strand coordinates, but the list of start
positions of the blocks within each alignment uses - strand coordinates.
This can be confusing.
 
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, Sep 5, 2014 at 7:33 AM, Alireza Fotuhi Siahpirani <
Matthew Speir <mspeir <at> soe.ucsc.edu>: Sep 05 11:10AM -0700

Hello Fei,
 
Thank you for your question about visualizing Multiz alignments. We
recommend using the UCSC Genome Browser to visualize your alignments. If
you have your alignments in MAF format, and we host the assembly used
for the alignment, you can upload these alignments as a custom track.
For more information on the MAF format, refer to the following help
page: http://genome.ucsc.edu/FAQ/FAQformat.html#format5. More
information on uploading custom tracks can be found here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html.
 
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 9/4/14, 4:21 PM, Liu, Fei wrote:
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genome | 28 Aug 19:13 2014

Digest for genome <at> soe.ucsc.edu - 6 updates in 5 topics

"Simonson, Tatum" <tsimonson <at> mail.ucsd.edu>: Aug 28 10:05AM

Thank you for your quick response, Steve.
 
We will reference the links and the manuscript associated with these data.
 
Sincerely,
Tatum
________________________________________
From: Steve Heitner [steve <at> soe.ucsc.edu]
Sent: Monday, August 25, 2014 11:06 AM
To: Simonson, Tatum; genome <at> soe.ucsc.edu
Cc: joseptarrago11 <at> gmail.com
Subject: RE: [genome] UCSC browser display of expression data
 
Hello, Tatum.
 
I would first like to point out that the link you provided is from our
official European mirror, http://genome-euro.ucsc.edu. I'm not certain if
you're intentionally using that mirror, but if not, our US site
(http://genome.ucsc.edu) would certainly be faster for you.
 
On the results page you mentioned, the data in the "Microarray Expression
Data" section comes from our GNF Atlas 2 track,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=gnfAtlas2. You can see
the equivalent GNF Atlas 2 results page for uc010aux.3 at
http://genome.ucsc.edu/cgi-bin/hgc?c=chr14&o=94844709&t=94849578&g=gnfAtlas2
&i=202833_s_at&i2=202833_s_at. I believe the description page and the color
key will help to answer your questions. On the UCSC Genes results page, the
"Absolute" data is just another representation of the "Ratios" data using a
different color scheme.
 
Please contact us again at genome <at> soe.ucsc.edu if you have any further
questions. Questions sent to that address will be archived in a
publicly-accessible forum for the benefit of other users. If your question
contains sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
 
---
Steve Heitner
UCSC Genome Bioinformatics Group
 
-----Original Message-----
From: Simonson, Tatum [mailto:tsimonson <at> mail.ucsd.edu]
Sent: Monday, August 25, 2014 9:07 AM
To: genome <at> soe.ucsc.edu
Cc: joseptarrago11 <at> gmail.com
Subject: [genome] UCSC browser display of expression data
 
Hi there,
 
I am working with students on the UCSD Genome Browser and have a few
questions regarding microarry data presented on the site (please see link
provided below for our gene of interest).
 
https://genome-euro.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc010aux.3&hgg_prot=P01
009&hgg_chrom=chr14&hgg_start=94843083&hgg_end=94857029&hgg_type=knownGene&d
b=hg19&hgsid=198846835_U1gmMFViIJiN78El0AmBYxlY04FQ
 
Is there a thorough description provided on the site or elsewhere as to how
the absolute and ratio data are determined and displayed other than "high"
and "low"?
What does the white to dark grey gradient indicate for absolute data (i.e.,
is this standardized for each tissue and compared relative to other
tissues)?
What criteria are used to determine high and low values (what is the
baseline used for comparison and again are these tissue-specific), and what
does a black box indicate (baseline or no data)?
 
Thank you in advance for your assistance!
 
Sincerely,
Tatum Simonson
 
--
Ya Hu <teresayahu <at> gmail.com>: Aug 28 03:50PM +0800

Dear sir or madam,
 
I am trying to check whether a mutation on a site is synonymous or
non-synonymous in human genome, (given position and allele status before
and after mutation), which files could I refer to from UCSC download site,
please?
 
Many thanks,
 
Ya Hu
Matthew Speir <mspeir <at> soe.ucsc.edu>: Aug 27 01:13PM -0700

Hi Fahad,
 
Thank you for your question about the LiftOver utility. Could you share
a few lines of the BED file you've been using as input for standalone
LiftOver? If you do not wish to share this information with the public
list, you can send them to me directly. This difference in output
coordinates is likely due to different input formats. The standalone
LiftOver utility takes bed format as input. The web LiftOver utility can
take both position and bed formats as input. Putting these two different
formats into the web LiftOver utility will give you different results.
This is because the position format is one-based and the bed format is
zero-based, and each one is interpreted by the Genome Browser
differently. You can read more about the differences between the two and
how they are interpreted by the Genome Browser here:
http://genome.ucsc.edu/FAQ/FAQtracks#tracks1.
 
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 8/21/14, 7:00 AM, Fahad Syed wrote:
Jeremy Johnson <jjohnson <at> broadinstitute.org>: Aug 28 09:13AM -0400

Hi Fahad,
 
A few things:
 
1) We're not responsible for maintaining in UCSC's tools. I suggest you
bring this up with them (genome <at> soe.ucsc.edu), but 1-off problems are
quite common when dealing with genomic data (computer science people like
to start numbering at 0, biologists at 1.)
 
2) We've already done this liftover, and have the data hosted on the
CanFam3.1 genome on UCSC via a Track Hub. If you go to UCSC, load the
CanFam3.1 assembly, the hit the "Track Hubs" button and load the "Broad
Improved Canine Annotation v1
<https://www.broadinstitute.org/ftp/pub/vgb/dog/trackHub/hub.txt>" Track
hub, there is a track there listed as "Survey SNPs." These contain the
SNPs from CanFam2, as well as some addition SNPs we generated when we
designed the dog SNP array.
 
3) You can check the results yourself between the discrepent tools, as you
have the truth set of genotypes from CanFam2. Whichever result matches
those genotypes (i.e. returns the same bases from CanFam3.1) is the correct
tool.
 
Hope this helps, and good luck!
 
~Jeremy
 
 
Jeremy Johnson
Project Coordinator
Vertebrate Biology Group
Broad Institute
 
Tel: (617) 714-7935
Brian Lee <brianlee <at> soe.ucsc.edu>: Aug 27 10:46AM -0700

Dear Gert,
 
Thank you for using the UCSC Genome Browser and your message about the
dragAndDrop documentation.
 
The notation in the documentation should read "dragAndDrop subTracks" and
is being updated, thank you for bringing this to our attention!
 
Thank you again for using and helping to improve the UCSC Genome Browser.
If you have any further questions, please reply togenome <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 Wed, Aug 27, 2014 at 8:40 AM, Gert Hulselmans <hulselmansgert <at> gmail.com>
wrote:
 
robert kuhn <kuhn <at> soe.ucsc.edu>: Aug 27 10:36AM -0700

Hello, Emma,
 
> I do think this is inconvenient... but I assume there are technical
reasons
> behind it.
 
We agree that this situation is inconvenient, but thanks for understanding.
We built genome-euro to make genome browsing faster over there, and
carefully considered the tradeoffs between allowing the two machines to
diverge at the Session-storage function vs keeping them in sync.
 
Because we believed that most researchers would use one or the other
machine and not very often find themselves on the other machine, the cost
of the very large storage and transmission to keep them in sync was not
justified. Our hosts at the University of Bielefeld are generous with
their
support of the European mirror, and we chose to not stress their bandwidth
with the constant syncing of data between the two sites.
 
We were about to contact you again to suggest that you sync up your
sessions in one place using save/reload, but are happy to see that you
found that solution on your own.
 
best regards, and thanks for using the Genome Browser.
 
--b0b kuhn
ucsc genome bioinformatics group
 
On 8/27/2014 12:17 AM, Emma Ivansson wrote:
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genome | 23 Aug 19:06 2014

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

Matthew Speir <mspeir <at> soe.ucsc.edu>: Aug 22 04:54PM -0700

Hi Anton,
 
We have been unable to replicate this issue on our end. Is it possible
that you are using a mirror site? Please confirm that you are using our
main site at http://genome.ucsc.edu/, or our European site at
http://genome-euro.ucsc.edu/. If you are using one of these two sites,
could you please provide us with your browser and operating system
information? Also, could you provide us with a detailed set of
instructions so that we can try to replicate this issue ourselves?
 
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 8/21/14, 9:45 PM, Anton Kratz wrote:
Steve Fischer <sfischer <at> upenn.edu>: Aug 22 06:41PM -0400

Hi,
 
We are evaluating a number of genome browser systems, such as UCSC
Browser, JBrowse and GenomeViewer for use as the Genome Browser on the
EuPathDB websites. These sites are databases that hold genome
information for parasites.
 
As part of our evaluation we like to look at sites, besides the main
UCSC Browser and mirrors, that use this software. I am having trouble
finding examples. Can you refer me to any?
 
Thanks,
Steve
 
--
~~~ *><>* ~~~
Robert Kuhn <kuhn <at> soe.ucsc.edu>: Aug 22 04:35PM -0700

Hi, Steve,
 
You probably want to post this to the genome-mirror mailing list.
Then people who are mirroring the Browser are likely to see it and
can contact you with their URLs.
 
Or you could look in the genome-mirror list archives:
 
https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror
 
Alternatively, you should consider using the Assembly Hubs mechansim,
which allows users to put their genomes on our public instance of the
Browser without downloading or installing the code locally. In that case,
you simply host the relevant files to make your own assembly.
 
The following link:
 
http://genome.ucsc.edu/cgi-bin/hgHubConnect
 
goes to a page with a further link to the User's Guide as well as offering
several remotely-hosted non-UCSC genome assemblies, such as Arabidopsis.
and Drosophila simulans for you to look at.
 
regards,
 
--b0b kuhn
ucsc genome bioinformatics group
 
 
 
Matthew Speir <mspeir <at> soe.ucsc.edu>: Aug 22 04:08PM -0700

Hi Alireza,
 
Thank you for your question about using the mm9 and hg19 pairwise
alignment files. Please see this previously answered mailing list
question for instructions on how to extract the alignments for your
regions of interest here:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/tOEkoCYem3c/3FMCjaxVQGUJ.
While that answer is dealing with danRer7 and hg19, you can easily
replace any reference to a danRer7 file with an equivalent file in mm9.
You can find the mm9 2bit file here:
http://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit, and the
hg19/mm9 pairwise alignment file here:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/vsMm9/hg19.mm9.all.chain.gz.
You can find the twoBitInfo, chainToAxt, axtToMaf, and mafsInRegion
utilities referenced in those instructions under the directory for your
system here: http://hgdownload.soe.ucsc.edu/admin/exe/.
 
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 8/21/14, 4:45 PM, Alireza Fotuhi Siahpirani wrote:
Matthew Speir <mspeir <at> soe.ucsc.edu>: Aug 22 01:39PM -0700

Hi Venkat,
 
Thank you for your question about converting Illumina exm IDs. I'm not
familiar with exm IDs, and I couldn't find any information on them after
some web searches. I would suggest you contact Illumina, the creators of
the OmniExpressExome chip, for an explanation of what these exm IDs
represent. You can find contact information for their customer support
here: http://www.illumina.com/company/contact-us.ilmn. If you can
provide me with a few sample lines from your file that contains these
IDs and their positions, I may be able to suggest a technique for using
the Genome Browser to convert them. If this file contains private
information that you do not wish to share with the public list, you may
send the file to me directly.
 
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 8/21/14, 9:49 AM, Venkat Addala wrote:
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genome | 8 Aug 19:24 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

    Matthew Speir <mspeir <at> soe.ucsc.edu> Aug 07 04:35PM -0700  

    Hello Vikram,
     
    Thank you for your question about the bedDetail format. You are allowed
    to keep multiple IDs in the ID column. These IDs can be separated by
    spaces, commas, or nearly anything except a tab. The tab separator is
    reserved for separating the columns themselves. If you intend to use the
    bedDetail format, you should use the ID column as the Genome Browser
    expects this column to be there.
     
    You may also want to consider using the bigBed format,
    http://genome.ucsc.edu/goldenPath/help/bigBed.html, for your data. The
    bigBed format has a few advantages over the bed and bedDetail formats.
    First, it is a compressed binary format, which means that the final
    files are going to be smaller than your standard bedDetail files.
    Second, you can use a custom AutoSql (.as) file to define as many extra
    columns as you would like. This means that you can define DOI, OMIM,
    etc. columns for your bigBed file. See "Example 3" on the bigBed format
    description page,
    http://genome.ucsc.edu/goldenPath/help/bigBed.html#Ex3, for more
    information on creating bigBed files from your bedDetail file and a
    custom .as file. You can download the bedToBigBed utility described on
    that page from the appropriate directory for your system here:
    http://hgdownload.soe.ucsc.edu/admin/exe/.
     
    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 7/31/14, 3:03 PM, Vikram Katju wrote:

     

    Debra Klopfenstein <note2debra <at> gmail.com> Aug 07 04:25PM -0400  

    Hello Everyone,
     
    I see in the cytoband file (from
    http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz)
    that there are several categories of data. What is the difference between
    "gvar" and "stalk". And "acen" is just centromeres?
     
    Thank you very much for all the great data and help.
     
    Best Wishes,
     
    Debra

     

    Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Aug 07 11:37AM -0700  

    Hello Matteo,
     
    Thanks for your question. You can access our public MySQL server directly (
    http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29) and query the
    trackDb table for any database (hg19, for example) to obtain track names
    and their associated tables. Here's the schema for trackDb:
    http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=hg19&hgta_doSchemaTable=trackDb.The
    RMySQL package in R should allow you to connect to our MySQL databases.
     
    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 Fri, Aug 1, 2014 at 12:14 PM, Matteo D'Antonio <madantonio <at> ucsd.edu>
    wrote:
     

     

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genome | 4 Aug 19:17 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

    Brian Smith <bsmith030465 <at> gmail.com> Aug 04 08:42AM -0400  

    Thanks! Is there a manual or README file that will help me with the
    installation and usage?
     
    regards,
     
     
    On Fri, Aug 1, 2014 at 6:06 PM, Luvina Guruvadoo <luvina <at> soe.ucsc.edu>
    wrote:
     

     

    Nickolai Tchurikov <tchurikov <at> eimb.ru> Aug 04 12:35PM +0400  

    Dear Colleagues,
     
    During the last summer (2013) I used the track ChIA-PET from ENCODE/GIS-Ruan in the
    UCSC browser. In the corresponding GEO databases (GSE39495)it is
    indicated that "The protein factors displayed in the track include estrogen receptor
    alpha (ERa), RNA polymerase II (RNAPII), and CCCTC binding factor (CTCF).".
     
    Does it means that you used the mixture of three antibodies or you
    included the separate obtained final data on the same track?
     
    Nickolai.
     
     
    --
    Nickolai A. Tchurikov, M.D., Ph.D.,
    Department of Epigenetic Mechanisms of Gene Expression Regulation,
    Engelhardt Institute of Molecular Biology,
    Vavilov Str. 32, 119991 Moscow, Russia
    E-mail: tchurikov <at> eimb.ru
    Phone: +7-499-135-97-53; Fax: +7-499-135-14-05

     

    YANG LIU <ubcyliu <at> gmail.com> Aug 01 07:04PM -0700  

    Dear Sir/ Madam,
     
    I am now using the UCLA database instead of the UCSC database and wondering
    how to write a command to connect to the MySQL server for the UCLA. I
    expect the command format is like your example shown for a connection to
    the UCSC,
     
    mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A
     
     
    Regards,
     
    Nicolas

     

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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

     

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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:

     

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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
     
     

     

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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
     

     
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Gmane