g***@soe.ucsc.edu
2014-09-25 17:25:09 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
- Table browser download for previous Ensembl versions [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/bd7967d4eca08f9e
- Protein coding, RNA and pseudogene extraction [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/250bb4bb4ffd0d8f
- New zebrafish genome reference assembly GRCz10 now available [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/28ab35dc035c08c8
- Fox genome assembly [3 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d47399afa766522
- Chr17 [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a80c9debe9bcedc6
- Obtaining dbSNP data for hg19 reference [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/9fa58f4631d05039
=============================================================================
Topic: Table browser download for previous Ensembl versions
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/bd7967d4eca08f9e
=============================================================================
---------- 1 of 1 ----------
From: m bauer <***@gmail.com>
Date: Sep 25 10:15AM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/aeb73f38702f57f1
Dear Steve,
[apologies for resending, realized I had sent it to the wrong address]
many thanks for your swift reply. One quick follow-up question:
gtpToGenePred would be freely available to all users (ie including
commercial) as part of kent/sr/utils as stated on http://genome.ucsc.edu/
license/? I was unable to find an explicit listing of what binaries would
belong to kent/sr/utils, so I thought I'd double check with you guys.
Again, many thanks for your help,
Markus
=============================================================================
Topic: Protein coding, RNA and pseudogene extraction
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/250bb4bb4ffd0d8f
=============================================================================
---------- 1 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 24 05:56PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/8344484a7368be45
Hello Ankit,
Thank you for your question about obtaining lists of genes and positions
from the UCSC Table Browser. It is a bit difficult to answer your question
without more information. You are quite right that there are many options
in the Table Browser, but part of that is because there is so much data to
browse! To give an example, here is how to extract the coordinates of all
transcripts from the UCSC Genes track on the human hg19 genome assembly:
1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables
2. Select the following options:
Clade: Mammals
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Predictions
Track: UCSC Genes
Table: knownGene
Region: genome
Output format: BED - Browser Extensible Data
3. Click "get output"
4. On the next page, make sure that the option to create one BED record per
"Whole Gene" is selected.
5. Click "get BED".
The result will be a list of all of the transcripts from the UCSC Genes
track, one per line, in BED format (
http://genome.ucsc.edu/FAQ/FAQformat.html#format1). The first three fields
on each line are the chromosome, start position, and end position of the
item. This may not be exactly what you want, however, as this table
includes multiple transcripts for each gene. The knownCanonical table (also
part of the UCSC Genes track) is built to only contain one representative
transcript for each gene; perhaps that is a better fit for your needs.
Alternatively, the RefSeq Genes or GENCODE Genes tracks may be what you
want. GENCODE Genes, for instance, includes a track devoted specifically to
pseudogenes. You can click on the "describe table schema" button for a
track and scrolling down will give you a description of the track.
Alternatively, you can click on those track names on the main track browser
page (http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19) to see a description
of what kind of data they contain and how they were built.
Information about how to separate coding from non-coding transcripts is
included in the answer to this mailing list question:
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/MvUWeimZR3E/discussion
.
More generally, you may also be interested in the Table Browser
documentation at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html,
and the linked OpenHelix video tutorials. The OpenHelix tutorial that
presents the UCSC Table Browser can be found at
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28.
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
---------- 2 of 2 ----------
From: ***@imsc.res.in
Date: Sep 25 11:18AM +0530
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a34fb04ebc8acf98
Thank you very much for your kind response.
=============================================================================
Topic: New zebrafish genome reference assembly GRCz10 now available
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/28ab35dc035c08c8
=============================================================================
---------- 1 of 1 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 24 01:58PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1a47286e2e2a595e
Hello Jason,
Thank you for your question about the availability of the Zv10 genome
assembly. We have plans to add this assembly to our browser and it does
have a high priority for us, but we do not yet have a timetable for when it
will be ready. Prior to release, a test browser will go up at
http://genome-test.soe.ucsc.edu. You are welcome to use the test browser
when it becomes available, with the proviso that it is still a test server:
much of the data will not have gone through our quality review process and
may be subject to change.
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 23, 2014 at 1:56 PM, Williams, Jason (SOP) <
=============================================================================
Topic: Fox genome assembly
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d47399afa766522
=============================================================================
---------- 1 of 3 ----------
From: "Kukekova, Anna V" <***@illinois.edu>
Date: Sep 24 07:54PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6ad88d468fb98b07
Dear UCSC Genome Browser team,
I would like to contact you about an opportunity to submit assembled genome of the red fox (Vulpes vulpes) to UCSC Genome Browser and make it available for the scientific community. The fox genome was sequenced and assembled at BGI and currently we are preparing a collaborative publication which describes this assembly.
I would very much appreciate your advise on it.
Thank you,
Anna
Anna Kukekova
Assistant Professor
Department of Animal Sciences
The University of Illinois at Urbana-Champaign
206 Edward R. Madigan Laboratory
1201 West Gregory Drive
Urbana, IL 61801
Phone: 217-300-2425
Fax: 217-244-5617
---------- 2 of 3 ----------
From: Luvina Guruvadoo <***@soe.ucsc.edu>
Date: Sep 24 01:24PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/58bc6b9648694b33
Hello Anna,
Thank you for your interest in the Genome Browser. Our agreement with
Ensembl and the genomics community is that we wait until an assembly has
been deposited into GenBank at NCBI before considering it for the Browser:
http://www.ncbi.nlm.nih.gov/genome/assembly/
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/
In the meantime, you are welcome to create an assembly hub which will allow
you to display your own genome assemblies and accompanying annotation
tracks in the UCSC Genome Browser. Please have a look through the following
page for more details and instructions on how to create an assembly hub:
http://genomewiki.ucsc.edu/index.php/Assembly_Hubs.
If you have any further questions, please reply to ***@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-***@soe.ucsc.edu.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
---------- 3 of 3 ----------
From: "Kukekova, Anna V" <***@illinois.edu>
Date: Sep 24 08:41PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/c9df0a499f7479e
Dear Luvina,
Thank you so much for clarifications. We will use the strategy you suggested.
All the best,
Anna
From: Luvina Guruvadoo <***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>>
Date: Wednesday, September 24, 2014 3:24 PM
To: Anna Kukekova <***@illinois.edu<mailto:***@illinois.edu>>
Cc: "***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>" <***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>>
Subject: Re: [genome] Fox genome assembly
Hello Anna,
Thank you for your interest in the Genome Browser. Our agreement with Ensembl and the genomics community is that we wait until an assembly has been deposited into GenBank at NCBI before considering it for the Browser:
http://www.ncbi.nlm.nih.gov/genome/assembly/
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/
In the meantime, you are welcome to create an assembly hub which will allow you to display your own genome assemblies and accompanying annotation tracks in the UCSC Genome Browser. Please have a look through the following page for more details and instructions on how to create an assembly hub: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs.
If you have any further questions, please reply to ***@soe.ucsc.edu<mailto:***@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-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On Wed, Sep 24, 2014 at 12:54 PM, Kukekova, Anna V <***@illinois.edu<mailto:***@illinois.edu>> wrote:
Dear UCSC Genome Browser team,
I would like to contact you about an opportunity to submit assembled genome of the red fox (Vulpes vulpes) to UCSC Genome Browser and make it available for the scientific community. The fox genome was sequenced and assembled at BGI and currently we are preparing a collaborative publication which describes this assembly.
I would very much appreciate your advise on it.
Thank you,
Anna
Anna Kukekova
Assistant Professor
Department of Animal Sciences
The University of Illinois at Urbana-Champaign
206 Edward R. Madigan Laboratory
1201 West Gregory Drive
Urbana, IL 61801
Phone: 217-300-2425<tel:217-300-2425>
Fax: 217-244-5617<tel:217-244-5617>
--
=============================================================================
Topic: Chr17
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a80c9debe9bcedc6
=============================================================================
---------- 1 of 1 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Sep 24 10:14AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/869cc5c8ffd7329c
Hi Terri,
Thank you for your question about haplotype sequences in the hg19
assembly. Sequences such as the one you mentioned, chr17_ctg5_hap1, are
haplotype regions that offer alternative sequences for a particular
region of the genome. The NCBI Nucleotide entries,
http://www.ncbi.nlm.nih.gov/nuccore/GL000258.1 and
http://www.ncbi.nlm.nih.gov/nuccore/568335820, for the chr17_ctg5_hap1
region state that this region provides a representation for the H2
haplotype at the MAPT locus on chr17. If you have some sequence that is
homologous to the haplotype, then it's likely homologous to the region
in the reference sequence too, though that may not always be the case.
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
On 9/18/14, 11:21 AM, Marquardt, Terri wrote:
=============================================================================
Topic: Obtaining dbSNP data for hg19 reference
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/9fa58f4631d05039
=============================================================================
---------- 1 of 1 ----------
From: Luvina Guruvadoo <***@soe.ucsc.edu>
Date: Sep 24 10:23AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/50f7b23b001b12ef
Hello Giuseppe,
Thank you for contacting us. The SNP files located in this directory are
mapped to the hg19 assembly:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
<http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp$SNPBUILD.txt.gz>
We have not yet released SNP tracks for the hg38 assembly.
If you have any further questions, please reply to ***@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-***@soe.ucsc.edu.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On Wed, Sep 24, 2014 at 8:26 AM, Giuseppe Gallone <
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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
- Table browser download for previous Ensembl versions [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/bd7967d4eca08f9e
- Protein coding, RNA and pseudogene extraction [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/250bb4bb4ffd0d8f
- New zebrafish genome reference assembly GRCz10 now available [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/28ab35dc035c08c8
- Fox genome assembly [3 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d47399afa766522
- Chr17 [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a80c9debe9bcedc6
- Obtaining dbSNP data for hg19 reference [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/9fa58f4631d05039
=============================================================================
Topic: Table browser download for previous Ensembl versions
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/bd7967d4eca08f9e
=============================================================================
---------- 1 of 1 ----------
From: m bauer <***@gmail.com>
Date: Sep 25 10:15AM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/aeb73f38702f57f1
Dear Steve,
[apologies for resending, realized I had sent it to the wrong address]
many thanks for your swift reply. One quick follow-up question:
gtpToGenePred would be freely available to all users (ie including
commercial) as part of kent/sr/utils as stated on http://genome.ucsc.edu/
license/? I was unable to find an explicit listing of what binaries would
belong to kent/sr/utils, so I thought I'd double check with you guys.
Again, many thanks for your help,
Markus
=============================================================================
Topic: Protein coding, RNA and pseudogene extraction
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/250bb4bb4ffd0d8f
=============================================================================
---------- 1 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 24 05:56PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/8344484a7368be45
Hello Ankit,
Thank you for your question about obtaining lists of genes and positions
from the UCSC Table Browser. It is a bit difficult to answer your question
without more information. You are quite right that there are many options
in the Table Browser, but part of that is because there is so much data to
browse! To give an example, here is how to extract the coordinates of all
transcripts from the UCSC Genes track on the human hg19 genome assembly:
1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables
2. Select the following options:
Clade: Mammals
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Predictions
Track: UCSC Genes
Table: knownGene
Region: genome
Output format: BED - Browser Extensible Data
3. Click "get output"
4. On the next page, make sure that the option to create one BED record per
"Whole Gene" is selected.
5. Click "get BED".
The result will be a list of all of the transcripts from the UCSC Genes
track, one per line, in BED format (
http://genome.ucsc.edu/FAQ/FAQformat.html#format1). The first three fields
on each line are the chromosome, start position, and end position of the
item. This may not be exactly what you want, however, as this table
includes multiple transcripts for each gene. The knownCanonical table (also
part of the UCSC Genes track) is built to only contain one representative
transcript for each gene; perhaps that is a better fit for your needs.
Alternatively, the RefSeq Genes or GENCODE Genes tracks may be what you
want. GENCODE Genes, for instance, includes a track devoted specifically to
pseudogenes. You can click on the "describe table schema" button for a
track and scrolling down will give you a description of the track.
Alternatively, you can click on those track names on the main track browser
page (http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19) to see a description
of what kind of data they contain and how they were built.
Information about how to separate coding from non-coding transcripts is
included in the answer to this mailing list question:
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/MvUWeimZR3E/discussion
.
More generally, you may also be interested in the Table Browser
documentation at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html,
and the linked OpenHelix video tutorials. The OpenHelix tutorial that
presents the UCSC Table Browser can be found at
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28.
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
---------- 2 of 2 ----------
From: ***@imsc.res.in
Date: Sep 25 11:18AM +0530
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a34fb04ebc8acf98
Thank you very much for your kind response.
=============================================================================
Topic: New zebrafish genome reference assembly GRCz10 now available
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/28ab35dc035c08c8
=============================================================================
---------- 1 of 1 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 24 01:58PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1a47286e2e2a595e
Hello Jason,
Thank you for your question about the availability of the Zv10 genome
assembly. We have plans to add this assembly to our browser and it does
have a high priority for us, but we do not yet have a timetable for when it
will be ready. Prior to release, a test browser will go up at
http://genome-test.soe.ucsc.edu. You are welcome to use the test browser
when it becomes available, with the proviso that it is still a test server:
much of the data will not have gone through our quality review process and
may be subject to change.
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 23, 2014 at 1:56 PM, Williams, Jason (SOP) <
=============================================================================
Topic: Fox genome assembly
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d47399afa766522
=============================================================================
---------- 1 of 3 ----------
From: "Kukekova, Anna V" <***@illinois.edu>
Date: Sep 24 07:54PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6ad88d468fb98b07
Dear UCSC Genome Browser team,
I would like to contact you about an opportunity to submit assembled genome of the red fox (Vulpes vulpes) to UCSC Genome Browser and make it available for the scientific community. The fox genome was sequenced and assembled at BGI and currently we are preparing a collaborative publication which describes this assembly.
I would very much appreciate your advise on it.
Thank you,
Anna
Anna Kukekova
Assistant Professor
Department of Animal Sciences
The University of Illinois at Urbana-Champaign
206 Edward R. Madigan Laboratory
1201 West Gregory Drive
Urbana, IL 61801
Phone: 217-300-2425
Fax: 217-244-5617
---------- 2 of 3 ----------
From: Luvina Guruvadoo <***@soe.ucsc.edu>
Date: Sep 24 01:24PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/58bc6b9648694b33
Hello Anna,
Thank you for your interest in the Genome Browser. Our agreement with
Ensembl and the genomics community is that we wait until an assembly has
been deposited into GenBank at NCBI before considering it for the Browser:
http://www.ncbi.nlm.nih.gov/genome/assembly/
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/
In the meantime, you are welcome to create an assembly hub which will allow
you to display your own genome assemblies and accompanying annotation
tracks in the UCSC Genome Browser. Please have a look through the following
page for more details and instructions on how to create an assembly hub:
http://genomewiki.ucsc.edu/index.php/Assembly_Hubs.
If you have any further questions, please reply to ***@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-***@soe.ucsc.edu.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
---------- 3 of 3 ----------
From: "Kukekova, Anna V" <***@illinois.edu>
Date: Sep 24 08:41PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/c9df0a499f7479e
Dear Luvina,
Thank you so much for clarifications. We will use the strategy you suggested.
All the best,
Anna
From: Luvina Guruvadoo <***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>>
Date: Wednesday, September 24, 2014 3:24 PM
To: Anna Kukekova <***@illinois.edu<mailto:***@illinois.edu>>
Cc: "***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>" <***@soe.ucsc.edu<mailto:***@soe.ucsc.edu>>
Subject: Re: [genome] Fox genome assembly
Hello Anna,
Thank you for your interest in the Genome Browser. Our agreement with Ensembl and the genomics community is that we wait until an assembly has been deposited into GenBank at NCBI before considering it for the Browser:
http://www.ncbi.nlm.nih.gov/genome/assembly/
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/
In the meantime, you are welcome to create an assembly hub which will allow you to display your own genome assemblies and accompanying annotation tracks in the UCSC Genome Browser. Please have a look through the following page for more details and instructions on how to create an assembly hub: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs.
If you have any further questions, please reply to ***@soe.ucsc.edu<mailto:***@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-***@soe.ucsc.edu<mailto:genome-***@soe.ucsc.edu>.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On Wed, Sep 24, 2014 at 12:54 PM, Kukekova, Anna V <***@illinois.edu<mailto:***@illinois.edu>> wrote:
Dear UCSC Genome Browser team,
I would like to contact you about an opportunity to submit assembled genome of the red fox (Vulpes vulpes) to UCSC Genome Browser and make it available for the scientific community. The fox genome was sequenced and assembled at BGI and currently we are preparing a collaborative publication which describes this assembly.
I would very much appreciate your advise on it.
Thank you,
Anna
Anna Kukekova
Assistant Professor
Department of Animal Sciences
The University of Illinois at Urbana-Champaign
206 Edward R. Madigan Laboratory
1201 West Gregory Drive
Urbana, IL 61801
Phone: 217-300-2425<tel:217-300-2425>
Fax: 217-244-5617<tel:217-244-5617>
--
=============================================================================
Topic: Chr17
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/a80c9debe9bcedc6
=============================================================================
---------- 1 of 1 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Sep 24 10:14AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/869cc5c8ffd7329c
Hi Terri,
Thank you for your question about haplotype sequences in the hg19
assembly. Sequences such as the one you mentioned, chr17_ctg5_hap1, are
haplotype regions that offer alternative sequences for a particular
region of the genome. The NCBI Nucleotide entries,
http://www.ncbi.nlm.nih.gov/nuccore/GL000258.1 and
http://www.ncbi.nlm.nih.gov/nuccore/568335820, for the chr17_ctg5_hap1
region state that this region provides a representation for the H2
haplotype at the MAPT locus on chr17. If you have some sequence that is
homologous to the haplotype, then it's likely homologous to the region
in the reference sequence too, though that may not always be the case.
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
On 9/18/14, 11:21 AM, Marquardt, Terri wrote:
=============================================================================
Topic: Obtaining dbSNP data for hg19 reference
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/9fa58f4631d05039
=============================================================================
---------- 1 of 1 ----------
From: Luvina Guruvadoo <***@soe.ucsc.edu>
Date: Sep 24 10:23AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/50f7b23b001b12ef
Hello Giuseppe,
Thank you for contacting us. The SNP files located in this directory are
mapped to the hg19 assembly:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
<http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp$SNPBUILD.txt.gz>
We have not yet released SNP tracks for the hg38 assembly.
If you have any further questions, please reply to ***@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-***@soe.ucsc.edu.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On Wed, Sep 24, 2014 at 8:26 AM, Giuseppe Gallone <
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