g***@soe.ucsc.edu
2014-10-14 17:05:42 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
- source doubts [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d2bdef65202782d9
- Clinical informations [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/89bea528cdc87de6
- GRC issues trackhub, please can you add to the Public hub list [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/19073c9719ad268d
- Need help with running BLAT too [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6727b8a42963e80
- miRNA sequence alignment in the Browser [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/92803a4f2191c8a1
- ensGene table for hg38 [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b8e44e66e79fc7f6
- patients with deletions of a specfic gene. [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7089bbe211acd38b
- No_chain_file_generation [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4290d0667603d2d
- Need help with running BLAT on CentOS [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
=============================================================================
Topic: source doubts
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d2bdef65202782d9
=============================================================================
---------- 1 of 1 ----------
From: "Elena De Mattia" <***@cro.it>
Date: Oct 14 03:58PM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/61920d6fffd92b64
Dear UCSC,
I'm 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) - 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=0
CB4QgQMwAA> 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: Clinical informations
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/89bea528cdc87de6
=============================================================================
---------- 1 of 1 ----------
From: Elisa Tassano <***@gmail.com>
Date: Oct 14 03:35PM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/580d86f6bd36e4aa
Dear,
I'm studing a patient with 6q21q22.1 microdeletion. I would know the
clinical informations of two patients reported on Decipher Database:
n.257884-n2498.
I attached a letter to send to these authors.
Thanks
Regards
Elisa Tassano
---------------------------------
Dott.ssa Elisa Tassano
Laboratorio di Citogenetica
Istituto Giannina Gaslini
Genova
***@gmail.com
tel.01056362267
=============================================================================
Topic: GRC issues trackhub, please can you add to the Public hub list
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/19073c9719ad268d
=============================================================================
---------- 1 of 1 ----------
From: Laura Clarke <***@ebi.ac.uk>
Date: Oct 14 01:10PM +0100
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/74d8e4055ac6d6a3
Hi
The GRC have established a trackhub to allow people to track
information about improvements to the human assembly
http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt
The Tracks are
* Genome issues under review by the GRC
* Genomic regions defined by the GRC
* Alignments between the primary assembly and alternate loci or patches
* Clone sequence anomalies
* Human regions with clones from the CHORI-17 library (CHM1tert)
Please let us know if you need any more info from us to add the hub
into the list
thanks
Laura
=============================================================================
Topic: Need help with running BLAT too
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6727b8a42963e80
=============================================================================
---------- 1 of 1 ----------
From: Niaina Rakotos <***@gmail.com>
Date: Oct 14 10:21AM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/fc30aa08481c7096
Hi guys,
I also tried to install blat35 (and blat34) on my MacOs , but I'vee got the
same error message as Aneesha
gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc
-I../../../../inc -I../../../../../inc -o xp.o -c xp.c
ar rcus /jkweb.a ...xmlEscape.o xp.o
ar: /jkweb.a: Permission denied
make[1]: *** [/jkweb.a] Erreur 1
make[1]: quittant le répertoire «
/pasteur/homes/nrakotos/MTBGenoomes/blatSrc/lib »
make: *** [all] Erreur 2
I am beginner in installing such programs and I would need also help from
you.
Niaina
=============================================================================
Topic: miRNA sequence alignment in the Browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/92803a4f2191c8a1
=============================================================================
---------- 1 of 1 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Oct 14 09:40AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/d5950ea61d1f1628
Hi Brid,
Thank you for your question about the sequence for the miRNA gene
hsa-mir-142. Based on your screenshot, I believe the issue is the
hsa-mir-142 gene is on the minus strand, but the Genome Browser is
displaying the sequence for the plus strand. If you view the sequence
for the minus strand, you should see that what's displayed in the Genome
Browser matches what is in the miRBase entry. Please see this answer to
a previous mailing list question for a great explanation of our strand
display for genes and how to view the minus strand in the Browser:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/_EjI7ddU_PY/O9UB7DwBvc8J.
I hope this is helpful. If you have any further questions, please reply
to ***@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 10/9/14, 3:06 PM, Ryan, Brid (NIH/NCI) [E] wrote:
=============================================================================
Topic: ensGene table for hg38
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b8e44e66e79fc7f6
=============================================================================
---------- 1 of 2 ----------
From: "Brockman, Joel" <***@thermofisher.com>
Date: Oct 13 05:38PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/88e060937aa36dd9
Hi,
Thank you for providing this great resource!
I would like to download the ensGene table for the hg38 assembly.
I've tried to obtain it using the Table Browser:
clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: All Tables
database: hg38
There is no "ensGene" in the drop down list for table.
I've also tried looking in http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/, but it's not there either.
Will you be making this table available any time soon?
Thanks again,
-Joel
---------- 2 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 13 02:49PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/b6c1127b4c7f0b4c
Hello, Joel.
The Ensembl Genes track has been replaced on hg38 with the GENCODE Genes
track as these two tracks have converged. When using the Table Browser,
select the Genes and Gene Predictions group and then select the GENCODE V20
track. Note that there are various tables available with GENCODE. For a
description of these, see the track description page at
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38
<http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV20>
&g=wgEncodeGencodeV20.
Please contact us again at ***@soe.ucsc.edu if you have any further
questions. All messages sent to that address are archived on a
publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Brockman, Joel [mailto:***@thermofisher.com]
Sent: Monday, October 13, 2014 2:38 PM
To: ***@soe.ucsc.edu
Subject: [genome] ensGene table for hg38
Hi,
Thank you for providing this great resource!
I would like to download the ensGene table for the hg38 assembly.
I've tried to obtain it using the Table Browser:
clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: All Tables
database: hg38
There is no "ensGene" in the drop down list for table.
I've also tried looking in
http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/, but it's not there
either.
Will you be making this table available any time soon?
Thanks again,
-Joel
--
=============================================================================
Topic: patients with deletions of a specfic gene.
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7089bbe211acd38b
=============================================================================
---------- 1 of 1 ----------
From: robert kuhn <***@soe.ucsc.edu>
Date: Oct 13 10:54AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6ef760e797c42be8
Hello, Peter,
We actually have a number of different datasets, so the answer might be
different for different sources. For example, the ISCA dataset does have
some clinical phenotypes, but they are often quite vague, such as
"developmental delay." For this dataset, it is possible to request,
through
the consortium website, www.iscaconsortium.org -- now iccg.org, for
contact with the clincial geneticist or attending physician. They will put
your request to the contributing labs and you must await their response.
To maintain the chain of confidentiality you do not have access to that
information.
For other datasets, you may be able to get more information by contacting
dbGaP at NCBI. The original record often contains more information than
we can display because of confidentiality. dbGaP allows access to those
who apply and convince them of a legitimate need.
I see you are in the Netherlands. In case you are not aware of it, I
want to
point you to the ECARUCA database,
http://umcecaruca01.extern.umcn.nl:8080/ecaruca/ecaruca.jsp
which has cases we do not.
best wishes and good luck in your efforts.
regards,
--b0b kuhn
ucsc genome bioinformatics group
On 10/8/2014 7:00 AM, Hasselt-2, P.M. van wrote:
=============================================================================
Topic: No_chain_file_generation
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4290d0667603d2d
=============================================================================
---------- 1 of 2 ----------
From: Irantzu Anzar <***@gmail.com>
Date: Oct 13 04:44PM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f67a92dcb02aae9f
Hi all,
I have a little question.
Why sometimes (in my case for some scaffolds), after running the liftover
available scripts (SameSpeciesBlatSetup.sh and SameSpeciesChainNet.sh), I
do not get any over.chain.gz file?
Thanks in advance,
Iran
---------- 2 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 13 10:41AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/4ebeb15017c35fd2
Hello, Iran.
When you say âsometimesâ, I assume that you have used the scripts to successfully obtain over.chain.gz files for other organisms and itâs not a question of proper usage. Itâs possible that in the cases where you do not get over.chain.gz files, the scaffolds do not align well enough to the other sequence to construct a liftOver.
Please contact us again at ***@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Irantzu Anzar [mailto:***@gmail.com]
Sent: Monday, October 13, 2014 7:44 AM
To: ***@soe.ucsc.edu
Subject: [genome] No_chain_file_generation
Hi all,
I have a little question.
Why sometimes (in my case for some scaffolds), after running the liftover available scripts (SameSpeciesBlatSetup.sh and SameSpeciesChainNet.sh), I do not get any over.chain.gz file?
Thanks in advance,
Iran
--
=============================================================================
Topic: Need help with running BLAT on CentOS
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
=============================================================================
---------- 1 of 1 ----------
From: Aneesha Das <***@gmail.com>
Date: Oct 11 11:39AM +0530
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/c5b8fee08f625a5c
Hi Jonathan,
When I type the command env CFLAGS="-E" make net.o in the blatSrc/lib/
folder, the following error message appears:
gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc
-I../../../../inc -c net.c
cc1: warnings being treated as errors
net.c: In function ânetAcceptingSocketFromâ:
net.c:92: error: pointer targets in passing argument 5 of âgetsockoptâ
differ in signedness
/usr/include/sys/socket.h:190: note: expected âsocklen_t * __restrict__â
but argument is of type âint *â
net.c: In function ânetAcceptâ:
net.c:115: error: pointer targets in passing argument 3 of âacceptâ differ
in signedness
/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â
but argument is of type âint *â
net.c: In function ânetAcceptFromâ:
net.c:130: error: pointer targets in passing argument 3 of âacceptâ differ
in signedness
/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â
but argument is of type âint *â
make: *** [net.o] Error 1
The net.o file was not generated. As per the instructions mentioned in the
PASA installation page (http://pasa.sourceforge.net/), the PASA software
package has to be moved to the location /usr/local/bin. Since PASA requires
blat, do we have to move the blast folder to the same location too? Please
let me know.
I have a request. I am quite ignorant about what each of the files in the
PASA lib directory contain, for example, I would like to know what
information the net.o file will contain. I request you to explain each step
that you carry out while debugging, if it is okay with you.
Regards,
Aneesha.
On Sat, Oct 11, 2014 at 6:21 AM, Jonathan Casper <***@soe.ucsc.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
- source doubts [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d2bdef65202782d9
- Clinical informations [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/89bea528cdc87de6
- GRC issues trackhub, please can you add to the Public hub list [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/19073c9719ad268d
- Need help with running BLAT too [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6727b8a42963e80
- miRNA sequence alignment in the Browser [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/92803a4f2191c8a1
- ensGene table for hg38 [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b8e44e66e79fc7f6
- patients with deletions of a specfic gene. [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7089bbe211acd38b
- No_chain_file_generation [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4290d0667603d2d
- Need help with running BLAT on CentOS [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
=============================================================================
Topic: source doubts
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d2bdef65202782d9
=============================================================================
---------- 1 of 1 ----------
From: "Elena De Mattia" <***@cro.it>
Date: Oct 14 03:58PM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/61920d6fffd92b64
Dear UCSC,
I'm 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) - 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=0
CB4QgQMwAA> 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: Clinical informations
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/89bea528cdc87de6
=============================================================================
---------- 1 of 1 ----------
From: Elisa Tassano <***@gmail.com>
Date: Oct 14 03:35PM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/580d86f6bd36e4aa
Dear,
I'm studing a patient with 6q21q22.1 microdeletion. I would know the
clinical informations of two patients reported on Decipher Database:
n.257884-n2498.
I attached a letter to send to these authors.
Thanks
Regards
Elisa Tassano
---------------------------------
Dott.ssa Elisa Tassano
Laboratorio di Citogenetica
Istituto Giannina Gaslini
Genova
***@gmail.com
tel.01056362267
=============================================================================
Topic: GRC issues trackhub, please can you add to the Public hub list
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/19073c9719ad268d
=============================================================================
---------- 1 of 1 ----------
From: Laura Clarke <***@ebi.ac.uk>
Date: Oct 14 01:10PM +0100
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/74d8e4055ac6d6a3
Hi
The GRC have established a trackhub to allow people to track
information about improvements to the human assembly
http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt
The Tracks are
* Genome issues under review by the GRC
* Genomic regions defined by the GRC
* Alignments between the primary assembly and alternate loci or patches
* Clone sequence anomalies
* Human regions with clones from the CHORI-17 library (CHM1tert)
Please let us know if you need any more info from us to add the hub
into the list
thanks
Laura
=============================================================================
Topic: Need help with running BLAT too
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6727b8a42963e80
=============================================================================
---------- 1 of 1 ----------
From: Niaina Rakotos <***@gmail.com>
Date: Oct 14 10:21AM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/fc30aa08481c7096
Hi guys,
I also tried to install blat35 (and blat34) on my MacOs , but I'vee got the
same error message as Aneesha
gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc
-I../../../../inc -I../../../../../inc -o xp.o -c xp.c
ar rcus /jkweb.a ...xmlEscape.o xp.o
ar: /jkweb.a: Permission denied
make[1]: *** [/jkweb.a] Erreur 1
make[1]: quittant le répertoire «
/pasteur/homes/nrakotos/MTBGenoomes/blatSrc/lib »
make: *** [all] Erreur 2
I am beginner in installing such programs and I would need also help from
you.
Niaina
=============================================================================
Topic: miRNA sequence alignment in the Browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/92803a4f2191c8a1
=============================================================================
---------- 1 of 1 ----------
From: Matthew Speir <***@soe.ucsc.edu>
Date: Oct 14 09:40AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/d5950ea61d1f1628
Hi Brid,
Thank you for your question about the sequence for the miRNA gene
hsa-mir-142. Based on your screenshot, I believe the issue is the
hsa-mir-142 gene is on the minus strand, but the Genome Browser is
displaying the sequence for the plus strand. If you view the sequence
for the minus strand, you should see that what's displayed in the Genome
Browser matches what is in the miRBase entry. Please see this answer to
a previous mailing list question for a great explanation of our strand
display for genes and how to view the minus strand in the Browser:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/_EjI7ddU_PY/O9UB7DwBvc8J.
I hope this is helpful. If you have any further questions, please reply
to ***@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 10/9/14, 3:06 PM, Ryan, Brid (NIH/NCI) [E] wrote:
=============================================================================
Topic: ensGene table for hg38
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b8e44e66e79fc7f6
=============================================================================
---------- 1 of 2 ----------
From: "Brockman, Joel" <***@thermofisher.com>
Date: Oct 13 05:38PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/88e060937aa36dd9
Hi,
Thank you for providing this great resource!
I would like to download the ensGene table for the hg38 assembly.
I've tried to obtain it using the Table Browser:
clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: All Tables
database: hg38
There is no "ensGene" in the drop down list for table.
I've also tried looking in http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/, but it's not there either.
Will you be making this table available any time soon?
Thanks again,
-Joel
---------- 2 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 13 02:49PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/b6c1127b4c7f0b4c
Hello, Joel.
The Ensembl Genes track has been replaced on hg38 with the GENCODE Genes
track as these two tracks have converged. When using the Table Browser,
select the Genes and Gene Predictions group and then select the GENCODE V20
track. Note that there are various tables available with GENCODE. For a
description of these, see the track description page at
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38
<http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV20>
&g=wgEncodeGencodeV20.
Please contact us again at ***@soe.ucsc.edu if you have any further
questions. All messages sent to that address are archived on a
publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Brockman, Joel [mailto:***@thermofisher.com]
Sent: Monday, October 13, 2014 2:38 PM
To: ***@soe.ucsc.edu
Subject: [genome] ensGene table for hg38
Hi,
Thank you for providing this great resource!
I would like to download the ensGene table for the hg38 assembly.
I've tried to obtain it using the Table Browser:
clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: All Tables
database: hg38
There is no "ensGene" in the drop down list for table.
I've also tried looking in
http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/, but it's not there
either.
Will you be making this table available any time soon?
Thanks again,
-Joel
--
=============================================================================
Topic: patients with deletions of a specfic gene.
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/7089bbe211acd38b
=============================================================================
---------- 1 of 1 ----------
From: robert kuhn <***@soe.ucsc.edu>
Date: Oct 13 10:54AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6ef760e797c42be8
Hello, Peter,
We actually have a number of different datasets, so the answer might be
different for different sources. For example, the ISCA dataset does have
some clinical phenotypes, but they are often quite vague, such as
"developmental delay." For this dataset, it is possible to request,
through
the consortium website, www.iscaconsortium.org -- now iccg.org, for
contact with the clincial geneticist or attending physician. They will put
your request to the contributing labs and you must await their response.
To maintain the chain of confidentiality you do not have access to that
information.
For other datasets, you may be able to get more information by contacting
dbGaP at NCBI. The original record often contains more information than
we can display because of confidentiality. dbGaP allows access to those
who apply and convince them of a legitimate need.
I see you are in the Netherlands. In case you are not aware of it, I
want to
point you to the ECARUCA database,
http://umcecaruca01.extern.umcn.nl:8080/ecaruca/ecaruca.jsp
which has cases we do not.
best wishes and good luck in your efforts.
regards,
--b0b kuhn
ucsc genome bioinformatics group
On 10/8/2014 7:00 AM, Hasselt-2, P.M. van wrote:
=============================================================================
Topic: No_chain_file_generation
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4290d0667603d2d
=============================================================================
---------- 1 of 2 ----------
From: Irantzu Anzar <***@gmail.com>
Date: Oct 13 04:44PM +0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f67a92dcb02aae9f
Hi all,
I have a little question.
Why sometimes (in my case for some scaffolds), after running the liftover
available scripts (SameSpeciesBlatSetup.sh and SameSpeciesChainNet.sh), I
do not get any over.chain.gz file?
Thanks in advance,
Iran
---------- 2 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Oct 13 10:41AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/4ebeb15017c35fd2
Hello, Iran.
When you say âsometimesâ, I assume that you have used the scripts to successfully obtain over.chain.gz files for other organisms and itâs not a question of proper usage. Itâs possible that in the cases where you do not get over.chain.gz files, the scaffolds do not align well enough to the other sequence to construct a liftOver.
Please contact us again at ***@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Irantzu Anzar [mailto:***@gmail.com]
Sent: Monday, October 13, 2014 7:44 AM
To: ***@soe.ucsc.edu
Subject: [genome] No_chain_file_generation
Hi all,
I have a little question.
Why sometimes (in my case for some scaffolds), after running the liftover available scripts (SameSpeciesBlatSetup.sh and SameSpeciesChainNet.sh), I do not get any over.chain.gz file?
Thanks in advance,
Iran
--
=============================================================================
Topic: Need help with running BLAT on CentOS
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
=============================================================================
---------- 1 of 1 ----------
From: Aneesha Das <***@gmail.com>
Date: Oct 11 11:39AM +0530
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/c5b8fee08f625a5c
Hi Jonathan,
When I type the command env CFLAGS="-E" make net.o in the blatSrc/lib/
folder, the following error message appears:
gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
-DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc
-I../../../../inc -c net.c
cc1: warnings being treated as errors
net.c: In function ânetAcceptingSocketFromâ:
net.c:92: error: pointer targets in passing argument 5 of âgetsockoptâ
differ in signedness
/usr/include/sys/socket.h:190: note: expected âsocklen_t * __restrict__â
but argument is of type âint *â
net.c: In function ânetAcceptâ:
net.c:115: error: pointer targets in passing argument 3 of âacceptâ differ
in signedness
/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â
but argument is of type âint *â
net.c: In function ânetAcceptFromâ:
net.c:130: error: pointer targets in passing argument 3 of âacceptâ differ
in signedness
/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â
but argument is of type âint *â
make: *** [net.o] Error 1
The net.o file was not generated. As per the instructions mentioned in the
PASA installation page (http://pasa.sourceforge.net/), the PASA software
package has to be moved to the location /usr/local/bin. Since PASA requires
blat, do we have to move the blast folder to the same location too? Please
let me know.
I have a request. I am quite ignorant about what each of the files in the
PASA lib directory contain, for example, I would like to know what
information the net.o file will contain. I request you to explain each step
that you carry out while debugging, if it is okay with you.
Regards,
Aneesha.
On Sat, Oct 11, 2014 at 6:21 AM, Jonathan Casper <***@soe.ucsc.edu>
wrote:
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