g***@soe.ucsc.edu
2014-10-17 17:10:42 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
- after output to a file, how can we reimport .gz (or decompressed) files? [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7628a50f5106a2cc
- I: [genome] source doubts [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/767bff71ae1b99a
- dbsnp 141 [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/5f414cf9a27f635d
- dbSNP 141 Data Download on UCSC FTP [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/5ec5139866659143
- Gencode Basic [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b0e16a885b88fb35
- Common TSS across different cell lines [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b878c05ea9742bca
- Problems with saved sessions [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/80f02072748f1f32
=============================================================================
Topic: after output to a file, how can we reimport .gz (or decompressed) files?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7628a50f5106a2cc
=============================================================================
---------- 1 of 1 ----------
From: Triantafillos Paparountas <***@bioinformatics.gr>
Date: Oct 17 03:18PM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/fc342872050b9fc0
Dear support,
I have stored the output of one query on the table browser as a .gz file.
How can I re-add it as a custom track?
The format of the text file within the .gz if I understand it is .bed, if I
remove the first line.
If I remember correctly bed file limits for upload are very strict but my
file is ~50kb
Should I convert it to bigbed ?
I believe this experience should have been easy since in effect I am
uploading the output of genome browser directly back to genome browser.
Thanks
--------------------------------------------------------------------------
Triantafyllos Paparountas, PhD
Bioinformatics Postdoctoral Researcher
Epigenetics and Genome Reprogramming lab
IRCCS Santa Lucia
Via del Fosso di Fiorano 64
00143 Rome, Italy
email: ***@bioinformatics.gr
Skype user id : triadafillos.paparountas
My linkedin profile:
http://gr.linkedin.com/in/paparountastriant/
--------------------------------------------------------------------------
=============================================================================
Topic: I: [genome] source doubts
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/767bff71ae1b99a
=============================================================================
---------- 1 of 1 ----------
From: "Elena De Mattia" <***@cro.it>
Date: Oct 17 11:13AM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/86717ebd2583cb3c
Thank you for your answer!
As you have request I sent you an example. We try to search the gene IL15RA using the NCBI36/hg18 (in attachment the imagine of the script). The web site return me the several messenger sequence but any gene sequence (NG_ or NC). I think that I have to set some parameter in order to obtained the gene sequence, Could you help me? Moreover, I use Hapmap to search and download the SNPs variant because I use Haploview for developing the haploblock. Unfortunately, the data of Hapmap are obsolete and in addition the variants catalogued derived from messenger and not from the sequence gene. Might you suggest me an alternative toll?
Thank you very much for your help!
RefSeq Genes
<http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6059580&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NM_172200,> IL15RA at chr10:6034340-6059580 - (NM_172200) interleukin-15 receptor subunit alpha isoform 2 precursor
<http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6059580&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NM_002189,> IL15RA at chr10:6034340-6059580 - (NM_002189) interleukin-15 receptor subunit alpha isoform 1 precursor
<http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6060156&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NM_001243539,> IL15RA at chr10:6034340-6060156 - (NM_001243539) interleukin-15 receptor subunit alpha isoform 3
<http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6059580&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NM_001256765,> IL15RA at chr10:6034340-6059580 - (NM_001256765) interleukin-15 receptor subunit alpha isoform 4
IL15RA at chr10:6034340-6060156 <http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6060156&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NR_046362,> - (NR_046362)
_____________________________________________________________________________
Elena De Mattia
De Mattia Elena
Medical Biotechnologist, Ph.D.
Experimental and Clinical Pharmacology Unit
<http://scholar.google.it/scholar?q=Department+of+Translational+research&hl=it&as_sdt=0&as_vis=1&lookup=0&oi=scholart&sa=X&ei=OZYzVKnCD8_ZasqmgegJ&ved=0CB4QgQMwAA> Department of Translational research
C.R.O.- IRCCS
via Franco Gallini, 2
33081 Aviano (PN), Italy
Tel +39-(0)434-659667
Fax +39-(0)434-659799
e-mail: <mailto:***@cro.it> ***@cro.it
Da: Jonathan Casper [mailto:***@soe.ucsc.edu]
Inviato: martedì 14 ottobre 2014 22.51
A: Elena De Mattia
Cc: ***@soe.ucsc.edu
Oggetto: Re: [genome] source doubts
Hello Elena,
Thank you for your question about gene searches. Can you give an example of a genome assembly (e.g., human GRCh38/hg38) and gene name (e.g., SIRT1) that you search for, and how you get sequence from UCSC? There are many ways to get sequence from UCSC; some of those ways return genomic sequence, and some of them return mRNA sequence (which might not be the same). Please note that UCSC often uses its own alignments, which might explain the difference in coordinates between UCSC, NCBI, and Ensembl. Are you also getting your HapMap and dbSNP data from our website? If so, which tracks are you using?
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, Oct 14, 2014 at 6:58 AM, Elena De Mattia <***@cro.it> wrote:
Dear UCSC,
Iâm Elena De Mattia, a PhD Fellow in the laboratory of Experimental and Clinical Pharmacology (Director Dr. Giuseppe Toffoli), Centro di Riferimento Oncologico (C.R.O) â IRCCS, Aviano (PN), Italy.
I'm working in the field of pharmacogenetics. For my work I have to perform a bio-informatic analysis in order to select the polymorphisms and subsequent the TagSnps of a candidate gene. I try to use some web database as UCSC, NCBI, Hapmap and Ensambl. I notice that Hapmap end UCSC, after insert the name of the gene in the search box, seem to return me the messenger sequence and the relative variant. Performing the same search in NCBI or Ensambl I find a different chromosomal coordinate that I supposed refer to the gene and not to the messenger. So I ask you:
1. A confirmation that these sites refer to different target (i.e. gene sequence or messenger sequence) to perform a gene and then polymorphisms search
2. If there is a way to choose of working on the gene sequence instead of mRNA sequence in Hapmap or UCSC.
A doubt, Hapmap containing only the variant in the mRNA coding sequence or also in the gene sequence?
Thanks you very much in advance for your help,
Elena De Mattia
_____________________________________________________________________________
Elena De Mattia
De Mattia Elena
Medical Biotechnologist, Ph.D.
Experimental and Clinical Pharmacology Unit
<http://scholar.google.it/scholar?q=Department+of+Translational+research&hl=it&as_sdt=0&as_vis=1&lookup=0&oi=scholart&sa=X&ei=OZYzVKnCD8_ZasqmgegJ&ved=0CB4QgQMwAA> Department of Translational research
C.R.O.- IRCCS
via Franco Gallini, 2
33081 Aviano (PN), Italy
Tel +39-(0)434-659667
Fax +39-(0)434-659799
e-mail: <mailto:***@cro.it> ***@cro.it
--
=============================================================================
Topic: dbsnp 141
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/5f414cf9a27f635d
=============================================================================
---------- 1 of 1 ----------
From: "da Silva, Cristina P." <***@emory.edu>
Date: Oct 17 02:05PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/25560a85232d7805
Hello,
We regularly use the dbsnp tables in UCSC (currently snp138). Do you have plans to make the dbSNP human build 141 available? Also, NCBI just release build 142 - I know it is early, but do you have plans for that?
Thanks,
Cristina da Silva
Bioinformatics Team
Emory Genetics Lab
Emory University
________________________________
This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.
If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
=============================================================================
Topic: dbSNP 141 Data Download on UCSC FTP
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/5ec5139866659143
=============================================================================
---------- 1 of 1 ----------
From: Ellen Schofield <***@cimr.cam.ac.uk>
Date: Oct 17 08:14AM +0100
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6854cc7c9371cd3e
Dear Sir/Madam,
I was wondering if you could give me a estimated time of availability
for the snp file for dbSNP141 to be available to download from your
website please? The equivalent to this file on hg19 -
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp138.txt.gz
Many thanks.
Yours,
Ellen.
--
***@cimr.cam.ac.uk
JDRF/Wellcome Trust Diabetes and Inflammation Laboratory,
NIHR Cambridge Biomedical Research Centre,
Cambridge Institute for Medical Research,
University of Cambridge,
WT/MRC Bldg, Addenbrooke's Hospital,
Hills Rd., Cambridge CB2 0XY UK
Tel: 01223 763215
=============================================================================
Topic: Gencode Basic
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b0e16a885b88fb35
=============================================================================
---------- 1 of 1 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Oct 16 05:07PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/8842aeeba2f5b3e
Hi Brendan,
Thank you for your question about the GENCODE Genes Basic set. The
GENCODE Basic set is described on the track description page,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV20.
The "Methods" section describes the criteria used for including a
transcript in the GENCODE Basic set.
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 10/16/14, 9:22 AM, Brendan Veeneman wrote:
=============================================================================
Topic: Common TSS across different cell lines
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b878c05ea9742bca
=============================================================================
---------- 1 of 1 ----------
From: ruvalcabatrejo <***@gmail.com>
Date: Oct 16 02:04PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/180345319eeb4146
Hello,
How do I find the most common Transcriptional Start Site across different
cell lines? I know how to find a TSS for a gene, but not the most common
TSS across different cell lines.
Thank you for your help!
Laura
=============================================================================
Topic: Problems with saved sessions
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/80f02072748f1f32
=============================================================================
---------- 1 of 1 ----------
From: Luvina Guruvadoo <***@soe.ucsc.edu>
Date: Oct 16 12:07PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/861cb9d09df272cc
Hello Nicola,
Are you using our European mirror site (http://genome-euro.ucsc.edu)? If
so, please view our documentation for more information about sessions and
custom tracks:
http://genome.ucsc.edu/goldenPath/help/genomeEuro.html#sessions.
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, Oct 15, 2014 at 6:33 AM, Festuccia Nicola <
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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
- after output to a file, how can we reimport .gz (or decompressed) files? [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7628a50f5106a2cc
- I: [genome] source doubts [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/767bff71ae1b99a
- dbsnp 141 [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/5f414cf9a27f635d
- dbSNP 141 Data Download on UCSC FTP [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/5ec5139866659143
- Gencode Basic [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b0e16a885b88fb35
- Common TSS across different cell lines [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b878c05ea9742bca
- Problems with saved sessions [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/80f02072748f1f32
=============================================================================
Topic: after output to a file, how can we reimport .gz (or decompressed) files?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7628a50f5106a2cc
=============================================================================
---------- 1 of 1 ----------
From: Triantafillos Paparountas <***@bioinformatics.gr>
Date: Oct 17 03:18PM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/fc342872050b9fc0
Dear support,
I have stored the output of one query on the table browser as a .gz file.
How can I re-add it as a custom track?
The format of the text file within the .gz if I understand it is .bed, if I
remove the first line.
If I remember correctly bed file limits for upload are very strict but my
file is ~50kb
Should I convert it to bigbed ?
I believe this experience should have been easy since in effect I am
uploading the output of genome browser directly back to genome browser.
Thanks
--------------------------------------------------------------------------
Triantafyllos Paparountas, PhD
Bioinformatics Postdoctoral Researcher
Epigenetics and Genome Reprogramming lab
IRCCS Santa Lucia
Via del Fosso di Fiorano 64
00143 Rome, Italy
email: ***@bioinformatics.gr
Skype user id : triadafillos.paparountas
My linkedin profile:
http://gr.linkedin.com/in/paparountastriant/
--------------------------------------------------------------------------
=============================================================================
Topic: I: [genome] source doubts
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/767bff71ae1b99a
=============================================================================
---------- 1 of 1 ----------
From: "Elena De Mattia" <***@cro.it>
Date: Oct 17 11:13AM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/86717ebd2583cb3c
Thank you for your answer!
As you have request I sent you an example. We try to search the gene IL15RA using the NCBI36/hg18 (in attachment the imagine of the script). The web site return me the several messenger sequence but any gene sequence (NG_ or NC). I think that I have to set some parameter in order to obtained the gene sequence, Could you help me? Moreover, I use Hapmap to search and download the SNPs variant because I use Haploview for developing the haploblock. Unfortunately, the data of Hapmap are obsolete and in addition the variants catalogued derived from messenger and not from the sequence gene. Might you suggest me an alternative toll?
Thank you very much for your help!
RefSeq Genes
<http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6059580&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NM_172200,> IL15RA at chr10:6034340-6059580 - (NM_172200) interleukin-15 receptor subunit alpha isoform 2 precursor
<http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6059580&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NM_002189,> IL15RA at chr10:6034340-6059580 - (NM_002189) interleukin-15 receptor subunit alpha isoform 1 precursor
<http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6060156&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NM_001243539,> IL15RA at chr10:6034340-6060156 - (NM_001243539) interleukin-15 receptor subunit alpha isoform 3
<http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6059580&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NM_001256765,> IL15RA at chr10:6034340-6059580 - (NM_001256765) interleukin-15 receptor subunit alpha isoform 4
IL15RA at chr10:6034340-6060156 <http://genome-euro.ucsc.edu/cgi-bin/hgTracks?position=chr10:6034340-6060156&hgsid=199559400_gIlfSyaCA2CG72KswZFgWa7i9P5H&refGene=pack&hgFind.matches=NR_046362,> - (NR_046362)
_____________________________________________________________________________
Elena De Mattia
De Mattia Elena
Medical Biotechnologist, Ph.D.
Experimental and Clinical Pharmacology Unit
<http://scholar.google.it/scholar?q=Department+of+Translational+research&hl=it&as_sdt=0&as_vis=1&lookup=0&oi=scholart&sa=X&ei=OZYzVKnCD8_ZasqmgegJ&ved=0CB4QgQMwAA> Department of Translational research
C.R.O.- IRCCS
via Franco Gallini, 2
33081 Aviano (PN), Italy
Tel +39-(0)434-659667
Fax +39-(0)434-659799
e-mail: <mailto:***@cro.it> ***@cro.it
Da: Jonathan Casper [mailto:***@soe.ucsc.edu]
Inviato: martedì 14 ottobre 2014 22.51
A: Elena De Mattia
Cc: ***@soe.ucsc.edu
Oggetto: Re: [genome] source doubts
Hello Elena,
Thank you for your question about gene searches. Can you give an example of a genome assembly (e.g., human GRCh38/hg38) and gene name (e.g., SIRT1) that you search for, and how you get sequence from UCSC? There are many ways to get sequence from UCSC; some of those ways return genomic sequence, and some of them return mRNA sequence (which might not be the same). Please note that UCSC often uses its own alignments, which might explain the difference in coordinates between UCSC, NCBI, and Ensembl. Are you also getting your HapMap and dbSNP data from our website? If so, which tracks are you using?
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, Oct 14, 2014 at 6:58 AM, Elena De Mattia <***@cro.it> wrote:
Dear UCSC,
Iâm Elena De Mattia, a PhD Fellow in the laboratory of Experimental and Clinical Pharmacology (Director Dr. Giuseppe Toffoli), Centro di Riferimento Oncologico (C.R.O) â IRCCS, Aviano (PN), Italy.
I'm working in the field of pharmacogenetics. For my work I have to perform a bio-informatic analysis in order to select the polymorphisms and subsequent the TagSnps of a candidate gene. I try to use some web database as UCSC, NCBI, Hapmap and Ensambl. I notice that Hapmap end UCSC, after insert the name of the gene in the search box, seem to return me the messenger sequence and the relative variant. Performing the same search in NCBI or Ensambl I find a different chromosomal coordinate that I supposed refer to the gene and not to the messenger. So I ask you:
1. A confirmation that these sites refer to different target (i.e. gene sequence or messenger sequence) to perform a gene and then polymorphisms search
2. If there is a way to choose of working on the gene sequence instead of mRNA sequence in Hapmap or UCSC.
A doubt, Hapmap containing only the variant in the mRNA coding sequence or also in the gene sequence?
Thanks you very much in advance for your help,
Elena De Mattia
_____________________________________________________________________________
Elena De Mattia
De Mattia Elena
Medical Biotechnologist, Ph.D.
Experimental and Clinical Pharmacology Unit
<http://scholar.google.it/scholar?q=Department+of+Translational+research&hl=it&as_sdt=0&as_vis=1&lookup=0&oi=scholart&sa=X&ei=OZYzVKnCD8_ZasqmgegJ&ved=0CB4QgQMwAA> Department of Translational research
C.R.O.- IRCCS
via Franco Gallini, 2
33081 Aviano (PN), Italy
Tel +39-(0)434-659667
Fax +39-(0)434-659799
e-mail: <mailto:***@cro.it> ***@cro.it
--
=============================================================================
Topic: dbsnp 141
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/5f414cf9a27f635d
=============================================================================
---------- 1 of 1 ----------
From: "da Silva, Cristina P." <***@emory.edu>
Date: Oct 17 02:05PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/25560a85232d7805
Hello,
We regularly use the dbsnp tables in UCSC (currently snp138). Do you have plans to make the dbSNP human build 141 available? Also, NCBI just release build 142 - I know it is early, but do you have plans for that?
Thanks,
Cristina da Silva
Bioinformatics Team
Emory Genetics Lab
Emory University
________________________________
This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.
If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
=============================================================================
Topic: dbSNP 141 Data Download on UCSC FTP
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/5ec5139866659143
=============================================================================
---------- 1 of 1 ----------
From: Ellen Schofield <***@cimr.cam.ac.uk>
Date: Oct 17 08:14AM +0100
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6854cc7c9371cd3e
Dear Sir/Madam,
I was wondering if you could give me a estimated time of availability
for the snp file for dbSNP141 to be available to download from your
website please? The equivalent to this file on hg19 -
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp138.txt.gz
Many thanks.
Yours,
Ellen.
--
***@cimr.cam.ac.uk
JDRF/Wellcome Trust Diabetes and Inflammation Laboratory,
NIHR Cambridge Biomedical Research Centre,
Cambridge Institute for Medical Research,
University of Cambridge,
WT/MRC Bldg, Addenbrooke's Hospital,
Hills Rd., Cambridge CB2 0XY UK
Tel: 01223 763215
=============================================================================
Topic: Gencode Basic
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b0e16a885b88fb35
=============================================================================
---------- 1 of 1 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Oct 16 05:07PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/8842aeeba2f5b3e
Hi Brendan,
Thank you for your question about the GENCODE Genes Basic set. The
GENCODE Basic set is described on the track description page,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV20.
The "Methods" section describes the criteria used for including a
transcript in the GENCODE Basic set.
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 10/16/14, 9:22 AM, Brendan Veeneman wrote:
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Topic: Common TSS across different cell lines
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b878c05ea9742bca
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From: ruvalcabatrejo <***@gmail.com>
Date: Oct 16 02:04PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/180345319eeb4146
Hello,
How do I find the most common Transcriptional Start Site across different
cell lines? I know how to find a TSS for a gene, but not the most common
TSS across different cell lines.
Thank you for your help!
Laura
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Topic: Problems with saved sessions
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/80f02072748f1f32
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From: Luvina Guruvadoo <***@soe.ucsc.edu>
Date: Oct 16 12:07PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/861cb9d09df272cc
Hello Nicola,
Are you using our European mirror site (http://genome-euro.ucsc.edu)? If
so, please view our documentation for more information about sessions and
custom tracks:
http://genome.ucsc.edu/goldenPath/help/genomeEuro.html#sessions.
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.
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Luvina Guruvadoo
UCSC Genome Bioinformatics Group
On Wed, Oct 15, 2014 at 6:33 AM, Festuccia Nicola <
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