g***@soe.ucsc.edu
2014-09-17 17:16:27 UTC
=============================================================================
Today's topic summary
=============================================================================
Group: ***@soe.ucsc.edu
Url:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/topics
- should be simple in table browser [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/321f65b11d9c4794
- Question regarding the UCSC genome browser [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d9f0c36e16e4d31f
- Converting genomic coordinates to cDNA coordinates [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c14272278f44ff51
- mysql connction [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/86e14d7cc5ce3b79
=============================================================================
Topic: should be simple in table browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/321f65b11d9c4794
=============================================================================
---------- 1 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Sep 16 02:35PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/d8f73daeb748b8d
Hello, Bill.
With the exception of retrieving sequence from the Table Browser where you
can add an optional description field into your input which gets inserted
into the FASTA headers of your output, the Table Browser is not designed to
include any input in the output. You will have to design a script to parse
and insert the appropriate information into your output.
You may also consider checking out Galaxy (https://usegalaxy.org/) to see if
they have any tools that would be useful to you in this regard.
Please contact us again 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-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: LaFramboise, William A [mailto:***@upmc.edu]
Sent: Sunday, September 14, 2014 5:25 AM
To: ***@soe.ucsc.edu; Matthew Speir
Subject: RE: [genome] should be simple in table browser
This solution worked nicely. One niggling issue--- I get many outputs
(multiple variants) for my entries but cannot align them with my original
entries since none of my input is retained in the output file. Is there a
simple way to retain one of my entry coordinates or add a series number to
the input to sort and align the output?
Thanks,
Bill.
________________________________________
From: Matthew Speir [***@soe.ucsc.edu]
Sent: Friday, September 12, 2014 6:41 PM
To: LaFramboise, William A; ***@soe.ucsc.edu
Subject: Re: [genome] should be simple in table browser
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
***@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-***@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
settings to reveal gene names associated with these positions?
--
---------- 2 of 2 ----------
From: "LaFramboise, William A" <***@upmc.edu>
Date: Sep 17 11:22AM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/538248bdc1d5a656
Thanks Steve.
Bill
-----Original Message-----
From: Steve Heitner [mailto:***@soe.ucsc.edu]
Sent: Tuesday, September 16, 2014 5:36 PM
To: LaFramboise, William A; ***@soe.ucsc.edu; 'Matthew Speir'
Subject: RE: [genome] should be simple in table browser
Hello, Bill.
With the exception of retrieving sequence from the Table Browser where you can add an optional description field into your input which gets inserted into the FASTA headers of your output, the Table Browser is not designed to include any input in the output. You will have to design a script to parse and insert the appropriate information into your output.
You may also consider checking out Galaxy (https://usegalaxy.org/) to see if they have any tools that would be useful to you in this regard.
Please contact us again 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-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: LaFramboise, William A [mailto:***@upmc.edu]
Sent: Sunday, September 14, 2014 5:25 AM
To: ***@soe.ucsc.edu; Matthew Speir
Subject: RE: [genome] should be simple in table browser
This solution worked nicely. One niggling issue--- I get many outputs (multiple variants) for my entries but cannot align them with my original entries since none of my input is retained in the output file. Is there a simple way to retain one of my entry coordinates or add a series number to the input to sort and align the output?
Thanks,
Bill.
________________________________________
From: Matthew Speir [***@soe.ucsc.edu]
Sent: Friday, September 12, 2014 6:41 PM
To: LaFramboise, William A; ***@soe.ucsc.edu
Subject: Re: [genome] should be simple in table browser
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 ***@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-***@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
--
=============================================================================
Topic: Question regarding the UCSC genome browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d9f0c36e16e4d31f
=============================================================================
---------- 1 of 1 ----------
From: "Jain, Nitika" <***@iupui.edu>
Date: Sep 16 04:41PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/cb5cd8264e079be8
Dear Sir/ Madam
I have been trying to find genes for the probe sets in a batch from
UCSC but not able to do so. I could only find the gene for one probeset
at a time. Kindly help me regarding that, as I have a list of more
than 1000 probesets and it is not possible to work on them one at a
time.
Thank you
Dr Nitika Jain
=============================================================================
Topic: Converting genomic coordinates to cDNA coordinates
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c14272278f44ff51
=============================================================================
---------- 1 of 2 ----------
From: Margaret Hoang <***@gmail.com>
Date: Sep 16 12:21PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f220746531f9ded7
Hi, I have the following information for mutations in GRCh37/hg19:
1. Transcript Accession
2. Gene Accession
3. Genomic Coordinate and Base sequence (i.e. g.chr1:2000-2000C>T)
Iâd like to express this as cDNA coordinates including the transcriptional base (i.e. c.190G>A).
Do you have suggestions on how to do this?
Thank you,
Margaret
~~~
Margaret Hoang, Ph.D.
Postdoctoral Fellow
Ludwig Center for Cancer Genetics and Therapeutics
The Sidney Kimmel Comprehensive Cancer Center
Johns Hopkins University, School of Medicine
1650 Orleans St., CRB1 Room 520, Baltimore, MD 21231
Office: 410-955-8878
Fax: 410-955-0548
Email: ***@gmail.com
---------- 2 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 16 01:39PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/346e2aa3eec40944
Hello Margaret,
Thank you for your question about converting genomic variants into other
formats. One of our engineers suggests that the following tool may provide
almost exactly what you need: https://mutalyzer.nl/positionConverter. You
would need to make some minor changes: the "g." should appear after the
colon (e.g., g.chr1:2000-2000C>T --> chr1:g.2000-2000C>T).
You may also be interested in our Variant Annotation Integrator (VAI) at
http://genome.ucsc.edu/cgi-bin/hgVai. With a list of variants in pgSNP or
VCF format, the VAI can provide coordinates for the variants in cDNA and
CDS for a variety of gene/transcript sets along with consequent changes to
the transcriptional base(s).
I hope this is helpful. If you have any further questions, please reply to
***@soe.ucsc.edu or genome-***@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-***@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
=============================================================================
Topic: mysql connction
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/86e14d7cc5ce3b79
=============================================================================
---------- 1 of 2 ----------
From: "Schmidt, Mike A" <***@med.miami.edu>
Date: Sep 16 07:17PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e08d39ae49d2da31
Hi,
I was trying to connect to your DB using the mysql client on my Windows7-64 machine but had no luck. See below...
[cid:***@01CFD1C1.5CDFAE10]
Any idea what I am doing wrong? I followed your instructions on:
http://genome.ucsc.edu/goldenPath/help/mysql.html
Thanks much
Mike Schmidt
---------- 2 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 16 12:31PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/69f6897e075891af
Hello Mike,
Thank you for your question about connecting to our public mysql server.
The problem appears to be that you are connecting to our mysql server as
"genome" without specifying a password, but mysql decides you're using a
password all the same (using password: YES). Do you have a mysql
configuration file set up with a default password? That might be
interfering. You can get around this by connecting as user "genomep" and
specifying the password "password".
I hope this is helpful. If you have any further questions, please reply to
***@soe.ucsc.edu or genome-***@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-***@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Sep 16, 2014 at 12:17 PM, Schmidt, Mike A <***@med.miami.edu>
wrote:
--
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Today's topic summary
=============================================================================
Group: ***@soe.ucsc.edu
Url:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/topics
- should be simple in table browser [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/321f65b11d9c4794
- Question regarding the UCSC genome browser [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d9f0c36e16e4d31f
- Converting genomic coordinates to cDNA coordinates [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c14272278f44ff51
- mysql connction [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/86e14d7cc5ce3b79
=============================================================================
Topic: should be simple in table browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/321f65b11d9c4794
=============================================================================
---------- 1 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Sep 16 02:35PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/d8f73daeb748b8d
Hello, Bill.
With the exception of retrieving sequence from the Table Browser where you
can add an optional description field into your input which gets inserted
into the FASTA headers of your output, the Table Browser is not designed to
include any input in the output. You will have to design a script to parse
and insert the appropriate information into your output.
You may also consider checking out Galaxy (https://usegalaxy.org/) to see if
they have any tools that would be useful to you in this regard.
Please contact us again 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-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: LaFramboise, William A [mailto:***@upmc.edu]
Sent: Sunday, September 14, 2014 5:25 AM
To: ***@soe.ucsc.edu; Matthew Speir
Subject: RE: [genome] should be simple in table browser
This solution worked nicely. One niggling issue--- I get many outputs
(multiple variants) for my entries but cannot align them with my original
entries since none of my input is retained in the output file. Is there a
simple way to retain one of my entry coordinates or add a series number to
the input to sort and align the output?
Thanks,
Bill.
________________________________________
From: Matthew Speir [***@soe.ucsc.edu]
Sent: Friday, September 12, 2014 6:41 PM
To: LaFramboise, William A; ***@soe.ucsc.edu
Subject: Re: [genome] should be simple in table browser
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
***@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-***@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
chr1 1288539 1288540
and get back the gene names and/or symbols encoded for each region.
Following your directions in the Table Browser and "help" list from
previous questions for submission of a list of positions I used theand get back the gene names and/or symbols encoded for each region.
Following your directions in the Table Browser and "help" list from
#name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts
exonEnds proteinID alignID
However, I cannot get gene names nor relate this back to my input file to
interrogate with the protein IDs. May I trouble you for insight as toexonEnds proteinID alignID
However, I cannot get gene names nor relate this back to my input file to
settings to reveal gene names associated with these positions?
--
---------- 2 of 2 ----------
From: "LaFramboise, William A" <***@upmc.edu>
Date: Sep 17 11:22AM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/538248bdc1d5a656
Thanks Steve.
Bill
-----Original Message-----
From: Steve Heitner [mailto:***@soe.ucsc.edu]
Sent: Tuesday, September 16, 2014 5:36 PM
To: LaFramboise, William A; ***@soe.ucsc.edu; 'Matthew Speir'
Subject: RE: [genome] should be simple in table browser
Hello, Bill.
With the exception of retrieving sequence from the Table Browser where you can add an optional description field into your input which gets inserted into the FASTA headers of your output, the Table Browser is not designed to include any input in the output. You will have to design a script to parse and insert the appropriate information into your output.
You may also consider checking out Galaxy (https://usegalaxy.org/) to see if they have any tools that would be useful to you in this regard.
Please contact us again 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-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: LaFramboise, William A [mailto:***@upmc.edu]
Sent: Sunday, September 14, 2014 5:25 AM
To: ***@soe.ucsc.edu; Matthew Speir
Subject: RE: [genome] should be simple in table browser
This solution worked nicely. One niggling issue--- I get many outputs (multiple variants) for my entries but cannot align them with my original entries since none of my input is retained in the output file. Is there a simple way to retain one of my entry coordinates or add a series number to the input to sort and align the output?
Thanks,
Bill.
________________________________________
From: Matthew Speir [***@soe.ucsc.edu]
Sent: Friday, September 12, 2014 6:41 PM
To: LaFramboise, William A; ***@soe.ucsc.edu
Subject: Re: [genome] should be simple in table browser
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 ***@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-***@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
chr1 1288539 1288540
and get back the gene names and/or symbols encoded for each region.
Following your directions in the Table Browser and "help" list from
exonEnds proteinID alignID
However, I cannot get gene names nor relate this back to my input file
to
interrogate with the protein IDs. May I trouble you for insight as to settings to reveal gene names associated with these positions?and get back the gene names and/or symbols encoded for each region.
Following your directions in the Table Browser and "help" list from
exonEnds proteinID alignID
However, I cannot get gene names nor relate this back to my input file
to
--
=============================================================================
Topic: Question regarding the UCSC genome browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d9f0c36e16e4d31f
=============================================================================
---------- 1 of 1 ----------
From: "Jain, Nitika" <***@iupui.edu>
Date: Sep 16 04:41PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/cb5cd8264e079be8
Dear Sir/ Madam
I have been trying to find genes for the probe sets in a batch from
UCSC but not able to do so. I could only find the gene for one probeset
at a time. Kindly help me regarding that, as I have a list of more
than 1000 probesets and it is not possible to work on them one at a
time.
Thank you
Dr Nitika Jain
=============================================================================
Topic: Converting genomic coordinates to cDNA coordinates
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c14272278f44ff51
=============================================================================
---------- 1 of 2 ----------
From: Margaret Hoang <***@gmail.com>
Date: Sep 16 12:21PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f220746531f9ded7
Hi, I have the following information for mutations in GRCh37/hg19:
1. Transcript Accession
2. Gene Accession
3. Genomic Coordinate and Base sequence (i.e. g.chr1:2000-2000C>T)
Iâd like to express this as cDNA coordinates including the transcriptional base (i.e. c.190G>A).
Do you have suggestions on how to do this?
Thank you,
Margaret
~~~
Margaret Hoang, Ph.D.
Postdoctoral Fellow
Ludwig Center for Cancer Genetics and Therapeutics
The Sidney Kimmel Comprehensive Cancer Center
Johns Hopkins University, School of Medicine
1650 Orleans St., CRB1 Room 520, Baltimore, MD 21231
Office: 410-955-8878
Fax: 410-955-0548
Email: ***@gmail.com
---------- 2 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 16 01:39PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/346e2aa3eec40944
Hello Margaret,
Thank you for your question about converting genomic variants into other
formats. One of our engineers suggests that the following tool may provide
almost exactly what you need: https://mutalyzer.nl/positionConverter. You
would need to make some minor changes: the "g." should appear after the
colon (e.g., g.chr1:2000-2000C>T --> chr1:g.2000-2000C>T).
You may also be interested in our Variant Annotation Integrator (VAI) at
http://genome.ucsc.edu/cgi-bin/hgVai. With a list of variants in pgSNP or
VCF format, the VAI can provide coordinates for the variants in cDNA and
CDS for a variety of gene/transcript sets along with consequent changes to
the transcriptional base(s).
I hope this is helpful. If you have any further questions, please reply to
***@soe.ucsc.edu or genome-***@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-***@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
=============================================================================
Topic: mysql connction
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/86e14d7cc5ce3b79
=============================================================================
---------- 1 of 2 ----------
From: "Schmidt, Mike A" <***@med.miami.edu>
Date: Sep 16 07:17PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e08d39ae49d2da31
Hi,
I was trying to connect to your DB using the mysql client on my Windows7-64 machine but had no luck. See below...
[cid:***@01CFD1C1.5CDFAE10]
Any idea what I am doing wrong? I followed your instructions on:
http://genome.ucsc.edu/goldenPath/help/mysql.html
Thanks much
Mike Schmidt
---------- 2 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 16 12:31PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/69f6897e075891af
Hello Mike,
Thank you for your question about connecting to our public mysql server.
The problem appears to be that you are connecting to our mysql server as
"genome" without specifying a password, but mysql decides you're using a
password all the same (using password: YES). Do you have a mysql
configuration file set up with a default password? That might be
interfering. You can get around this by connecting as user "genomep" and
specifying the password "password".
I hope this is helpful. If you have any further questions, please reply to
***@soe.ucsc.edu or genome-***@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-***@soe.ucsc.edu.
--
Jonathan Casper
UCSC Genome Bioinformatics Group
On Tue, Sep 16, 2014 at 12:17 PM, Schmidt, Mike A <***@med.miami.edu>
wrote:
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