g***@soe.ucsc.edu
2014-09-10 17:14:09 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
- hCD44v6 sequence [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/21cbf6f6e8556d77
- about gene sequence [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c4062283cfc10bb3
- sea urchin genome and RNA-seq data [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4669adac0758d966
- BAM file [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b0cc1c6f8abbc1d9
- Genome Build #37 [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/28757a88d0c65bbe
=============================================================================
Topic: hCD44v6 sequence
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/21cbf6f6e8556d77
=============================================================================
---------- 1 of 1 ----------
From: Anna Stornaiuolo <***@molmed.com>
Date: Sep 10 01:21PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a4d0126d27c468ec
Dear sir madam,
sorry if I disturb you but I am not able to download from the BLAT browser the complete cDNA sequence of the human CD44 gene variant 6 (CD44v6).
Could you help me please?
Thank you very much in advance
Sincerely yours
Anna
[cid:***@01CF9F6D.BAA5BF70]
Anna Stornaiuolo
Researcher
Via Olgettina, 58 - 20132 Milano (MI), Italy
Tel. +39 02 21277.331
Fax +39 02 21277.325
***@molmed.com<mailto:***@molmed.com>
www.molmed.com<http://www.molmed.com>
________________________________
La presente comunicazione, con le informazioni in essa contenute e ogni documento o file allegato, Ú strettamente riservata e soggetta alle garanzie che legano i rapporti tra le parti interessate. E' rivolta unicamente alla/e persona/e cui Ú indirizzata ed alle altre da questa autorizzata/e a riceverla. Se non siete i destinatari/autorizzati siete avvisati che qualsiasi azione, copia, comunicazione, divulgazione, o simili basate sul contenuto di tali informazioni Ú vietata e potrebbe essere contro la legge (art. 616 C.P., D.Lgs. n. 196/2003 Codice in materia di protezione dei dati personali).Se avete ricevuto questa comunicazione per errore, vi preghiamo di darne notizia al mittente e a mezzo telefono, fax o e-mail e di distruggere il messaggio e ogni file allegato senza farne copia alcuna o riprodurne in alcun modo il contenuto.
This e-mail message and any documents or files transmitted with it are strictly confidential and intended solely for the use of the individual to whom they are addressed or to others authorized by the addressee. If you are not the intended recipient please note that it is forbidden to copy, disseminate or distribute the information contained in this mail and could infringe the provisions contained in the Law on Protection of Personal Data. If you have received this e-mail by mistake please notify the sender by phone, fax or e-mail and delete the message and any attachments without copying or duplicating any part thereof.
=============================================================================
Topic: about gene sequence
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c4062283cfc10bb3
=============================================================================
---------- 1 of 1 ----------
From: diler us <***@hotmail.com>
Date: Sep 10 12:32PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6b6d285e3c648a03
Hi, I have a problem . I want to get my gene sequence from genome browser but I could not get it ....PLEASE SENT this protein's genomic sequence to my mail adresss. I reached the homo sapiens but could not reached in mus musculus
Pif(proteolysis inducing factor), mus musculus
=============================================================================
Topic: sea urchin genome and RNA-seq data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4669adac0758d966
=============================================================================
---------- 1 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 09 02:30PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/83d4b6079fb11ba4
Hello José,
Our preview browser is currently having some problems. The file server that
provides its data is being rebuilt right now, but this process is expected
to take a while (at least another week, and probably more). If you need
access to the strPur4 genome assembly, you can also find it on our active
development server at http://genome-test.soe.ucsc.edu. Please be aware that
this server is regularly updated with new features and data that may be
broken or incorrect - it is a work in progress. The advantage of the
genome-preview server (when it is working) is that it gives a more stable
view of data and features than genome-test.
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 9, 2014 at 2:50 AM, José Luis Gómez Skarmeta <***@upo.es>
wrote:
---------- 2 of 2 ----------
From: "José Luis Gómez Skarmeta" <***@upo.es>
Date: Sep 10 09:51AM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/bedf28cdc8415f2c
Many thanks Jonathan.
JL
José Luis Gómez-Skarmeta
Professor, Spanish Research Council (CSIC)
Centro Andaluz de BiologÃa del Desarrollo
CSIC/ Universidad Pablo de Olavide
Carretera de Utrera Km1
41013 Sevilla
Spain
Personal website
http://www.upo.es/CABD/GomezSkarmetaLab/index.html
CABD website
http://www.cabd.es/
Phone: 34-954348948
Fax: 34-954349376
email: ***@upo.es
=============================================================================
Topic: BAM file
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b0cc1c6f8abbc1d9
=============================================================================
---------- 1 of 1 ----------
From: Luca Cavallone <***@gmail.com>
Date: Sep 09 06:53PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/8b05b943fc9a44dc
Hi, my question is related to BAM files.
I understood thatthe way I should upload a BAM file is to link UCSC to a
URL page.
I dont haveit an apparently my institute is not going to create one for me.
I was planning to create through online offers.
I was wondering what in this case I should upload to the web page.. all the
10Gbyte file? in my case I have an exon sequencing data.. or am I allowed
to upload part of the BAM file?
hope my question was quite clear...Thanks!
luca
=============================================================================
Topic: Genome Build #37
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/28757a88d0c65bbe
=============================================================================
---------- 1 of 1 ----------
From: Michael Johnson <***@gmail.com>
Date: Sep 09 02:34PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e2a9db97b7e35d33
Hello,
I am trying to download the entire set of genes from the UCSC genome
(build #37) . I need the sequence data, with exons in upper case. Using
Table Browser, the only change I make from the default settings is the
output format is ³sequence² instead of ³all fields from selected table.²
Unfortunately, this query times out.
Is there a way to perform this same query from the publicly-available
mysql server?
Thanks,
Michael
--
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To unsubscribe from this group and stop receiving emails from it send an email to genome+***@soe.ucsc.edu.
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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
- hCD44v6 sequence [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/21cbf6f6e8556d77
- about gene sequence [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c4062283cfc10bb3
- sea urchin genome and RNA-seq data [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4669adac0758d966
- BAM file [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b0cc1c6f8abbc1d9
- Genome Build #37 [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/28757a88d0c65bbe
=============================================================================
Topic: hCD44v6 sequence
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/21cbf6f6e8556d77
=============================================================================
---------- 1 of 1 ----------
From: Anna Stornaiuolo <***@molmed.com>
Date: Sep 10 01:21PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a4d0126d27c468ec
Dear sir madam,
sorry if I disturb you but I am not able to download from the BLAT browser the complete cDNA sequence of the human CD44 gene variant 6 (CD44v6).
Could you help me please?
Thank you very much in advance
Sincerely yours
Anna
[cid:***@01CF9F6D.BAA5BF70]
Anna Stornaiuolo
Researcher
Via Olgettina, 58 - 20132 Milano (MI), Italy
Tel. +39 02 21277.331
Fax +39 02 21277.325
***@molmed.com<mailto:***@molmed.com>
www.molmed.com<http://www.molmed.com>
________________________________
La presente comunicazione, con le informazioni in essa contenute e ogni documento o file allegato, Ú strettamente riservata e soggetta alle garanzie che legano i rapporti tra le parti interessate. E' rivolta unicamente alla/e persona/e cui Ú indirizzata ed alle altre da questa autorizzata/e a riceverla. Se non siete i destinatari/autorizzati siete avvisati che qualsiasi azione, copia, comunicazione, divulgazione, o simili basate sul contenuto di tali informazioni Ú vietata e potrebbe essere contro la legge (art. 616 C.P., D.Lgs. n. 196/2003 Codice in materia di protezione dei dati personali).Se avete ricevuto questa comunicazione per errore, vi preghiamo di darne notizia al mittente e a mezzo telefono, fax o e-mail e di distruggere il messaggio e ogni file allegato senza farne copia alcuna o riprodurne in alcun modo il contenuto.
This e-mail message and any documents or files transmitted with it are strictly confidential and intended solely for the use of the individual to whom they are addressed or to others authorized by the addressee. If you are not the intended recipient please note that it is forbidden to copy, disseminate or distribute the information contained in this mail and could infringe the provisions contained in the Law on Protection of Personal Data. If you have received this e-mail by mistake please notify the sender by phone, fax or e-mail and delete the message and any attachments without copying or duplicating any part thereof.
=============================================================================
Topic: about gene sequence
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/c4062283cfc10bb3
=============================================================================
---------- 1 of 1 ----------
From: diler us <***@hotmail.com>
Date: Sep 10 12:32PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6b6d285e3c648a03
Hi, I have a problem . I want to get my gene sequence from genome browser but I could not get it ....PLEASE SENT this protein's genomic sequence to my mail adresss. I reached the homo sapiens but could not reached in mus musculus
Pif(proteolysis inducing factor), mus musculus
=============================================================================
Topic: sea urchin genome and RNA-seq data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4669adac0758d966
=============================================================================
---------- 1 of 2 ----------
From: Jonathan Casper <***@soe.ucsc.edu>
Date: Sep 09 02:30PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/83d4b6079fb11ba4
Hello José,
Our preview browser is currently having some problems. The file server that
provides its data is being rebuilt right now, but this process is expected
to take a while (at least another week, and probably more). If you need
access to the strPur4 genome assembly, you can also find it on our active
development server at http://genome-test.soe.ucsc.edu. Please be aware that
this server is regularly updated with new features and data that may be
broken or incorrect - it is a work in progress. The advantage of the
genome-preview server (when it is working) is that it gives a more stable
view of data and features than genome-test.
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 9, 2014 at 2:50 AM, José Luis Gómez Skarmeta <***@upo.es>
wrote:
---------- 2 of 2 ----------
From: "José Luis Gómez Skarmeta" <***@upo.es>
Date: Sep 10 09:51AM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/bedf28cdc8415f2c
Many thanks Jonathan.
JL
José Luis Gómez-Skarmeta
Professor, Spanish Research Council (CSIC)
Centro Andaluz de BiologÃa del Desarrollo
CSIC/ Universidad Pablo de Olavide
Carretera de Utrera Km1
41013 Sevilla
Spain
Personal website
http://www.upo.es/CABD/GomezSkarmetaLab/index.html
CABD website
http://www.cabd.es/
Phone: 34-954348948
Fax: 34-954349376
email: ***@upo.es
=============================================================================
Topic: BAM file
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b0cc1c6f8abbc1d9
=============================================================================
---------- 1 of 1 ----------
From: Luca Cavallone <***@gmail.com>
Date: Sep 09 06:53PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/8b05b943fc9a44dc
Hi, my question is related to BAM files.
I understood thatthe way I should upload a BAM file is to link UCSC to a
URL page.
I dont haveit an apparently my institute is not going to create one for me.
I was planning to create through online offers.
I was wondering what in this case I should upload to the web page.. all the
10Gbyte file? in my case I have an exon sequencing data.. or am I allowed
to upload part of the BAM file?
hope my question was quite clear...Thanks!
luca
=============================================================================
Topic: Genome Build #37
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/28757a88d0c65bbe
=============================================================================
---------- 1 of 1 ----------
From: Michael Johnson <***@gmail.com>
Date: Sep 09 02:34PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/e2a9db97b7e35d33
Hello,
I am trying to download the entire set of genes from the UCSC genome
(build #37) . I need the sequence data, with exons in upper case. Using
Table Browser, the only change I make from the default settings is the
output format is ³sequence² instead of ³all fields from selected table.²
Unfortunately, this query times out.
Is there a way to perform this same query from the publicly-available
mysql server?
Thanks,
Michael
--
You received this digest because you're subscribed to updates for this group. You can change your settings on the group membership page:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/join
.
To unsubscribe from this group and stop receiving emails from it send an email to genome+***@soe.ucsc.edu.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+***@soe.ucsc.edu.