Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• PhastCon scores? [1 Update]

Jackie Jia Zhou <dr.jzhou <at> gmail.com> May 10 01:36PM -0700  

Hi,
 
I downloaded the phastCon scores for rat with other 8 vertebrates from this
link : http://hgdownload.soe.ucsc.edu/goldenPath/rn4/phastCons9way/
I have a couple of questions regarding the files/scores:
1) There are many genomic regions (the genomic coordiates in these regions
are not in the downloaded files) that do not have a phastCon score in the
file, why is that? does that mean these regions are not conserved at all?
can I treat these regions as having a score=0 when handling the file?
2) Is there any threshold value for conservation score based on which we
can define a particular block of gene to be ideally conserved?
 
Thank you,
 
-Jackie


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• Percent DNase I Hypersensitive [1 Update]
• CDS does not start with ATG(140/36558) [1 Update]
• Installing kentsourcetools on Ma OS [2 Updates]
• personal Genome SNP format [1 Update]
• moving between hg36 and hg37 versions [1 Update]

Brian Lee <brianlee <at> soe.ucsc.edu> May 10 09:27AM -0700  

Dear David,
 
Thank you for using the UCSC Genome Browser and your appreciation of our
support. It is not readily clear what you may be attempting for your
research without examples.
 
Perhaps you may be submitting through the table browser a selection of
defined regions, and then perhaps clicking the "summary/statistics" button
against a DNase track to get desired output like "Item bases 2,128,151
(3.95%)"? There may be some technical solutions, depending on an
understanding of what you are attempting, however, they may be more
challenging to pursue for someone less familiar with computers as you
mentioned.
 
You might be interested in the DNase Clusters track,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegDnaseClusteredV2.
This track shows DNase hypersensitive areas assayed in a large collection
of cell types, aggregated and uniformly processed. In the table browser you
can select the "Regulation" group, "DNase Clusters" track, and the
"wgEncodeRegDnaseClusteredV2" table, and then click the "describe table
schema" button to learn more about this data in BED format.
 
If you created a custom track of your regions, one approach you can take is
to do an intersection of your data with the tables you may be interested
in, such as the wgEncodeRegDnaseClusteredV2 table. However, performing an
intersection with a custom track with 2.5 million regions using the Table
Browser will likely time out. To learn more about creating a custom track
please review the User Guide:
http://genome.ucsc.edu/goldenPath/help/customTrack.html, I also recommend
watching this Table Browser Custom Track tutorial:
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28. Also, read about
performing intersections with the Table Browser here:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection
 
More technical solutions could be to download some tools available from our
utilities directory, http://hgdownload.cse.ucsc.edu/admin/exe/,
specifically bigWigAverageOverBed. This program will complete an
intersection with a bed file and a bigWig file. Depending on what you are
attempting to do, you perhaps could also perform MySQL queries on the
tables of interest, please read more here:
http://genome.ucsc.edu/goldenPath/help/mysql.html
 
Without a clear picture of what you are attempting it is hard to direct you
on the best path. Thank you again for your inquiry and using the UCSC
Genome Browser. If you have further questions, please feel free to contact
the mailing list again at genome <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genome Bioinformatics Group
 
 
On Tue, May 7, 2013 at 12:09 PM, Rosenbaum, David J - (djr1) <


 

Pauline Fujita <pauline <at> soe.ucsc.edu> May 09 04:04PM -0700  

Hi Yi,
 
In the case of NM_001271872 the problem is that the human reference
hg19 has a deletion that includes the first exon of NM_001271872. This
has been repaired in a patch which you can see by turning on the "GRC
patch" and "GRC incident" tracks.
 
For the rest of the discrepancies you're seeing, they are likely to be
caused by a difference between the hg19 reference sequence and the
sequence of whomever contributed the mRNA to RefSeq (i.e. RefSeq
mRNA's come from many different individuals whose genome sequence
doesn't necessarily match the reference sequence, either because there
is an error in the assembly of the reference sequence, or because of
polymorphism in the population.)
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 


 

grant hartzog <hartzog <at> ucsc.edu> May 09 03:03PM -0700  

I am trying to install the kentsourcetools on my Mac (x86_64, OS 10.8.3) and am failing. It appears to be a problem with zlib, which is on my machine. Any clues as to what might be going wrong here?
 
I exported the following two variables
 
MYSQLLIBS="/usr/local/mysql/lib/libmysqlclient.a -lz"
MYSQLINC=/usr/local/mysql/include/mysql
 
and then did this:
 
dhcp-151-90:~ grant$ cd kent/src
dhcp-151-90:src grant$ make
cd lib && make
make[1]: `x86_64/jkweb.a' is up to date.
cd jkOwnLib && make
make[1]: `../lib/x86_64/jkOwnLib.a' is up to date.
cd hg/lib && make
make[1]: `../../lib/x86_64/jkhgap.a' is up to date.
mkdir -p /Users/grant/bin/scripts
mkdir -p /Users/grant/bin/x86_64
ameme
gcc -O -g -o /Users/grant/bin/x86_64/ameme ameme.o fragFind.o ../lib/x86_64/jkweb.a -pthread -lssl -lcrypto -lpng -lm -lm
true /Users/grant/bin/x86_64/ameme
 
[snip]
 
gcc -O -g -o /Users/grant/bin/x86_64/bigBedInfo bigBedInfo.o ../../lib/x86_64/jkweb.a -pthread -lssl -lcrypto -lpng -lm -lz -lm
true /Users/grant/bin/x86_64/bigBedInfo
bigBedNamedItems
gcc -O -g -o /Users/grant/bin/x86_64/bigBedNamedItems bigBedNamedItems.o ../../lib/x86_64/jkweb.a -pthread -lssl -lcrypto -lpng -lm -lm
Undefined symbols for architecture x86_64:
"_compress", referenced from:
_zCompress in jkweb.a(zlibFace.o)
_zSelfTest in jkweb.a(zlibFace.o)
"_uncompress", referenced from:
_zUncompress in jkweb.a(zlibFace.o)
_zSelfTest in jkweb.a(zlibFace.o)
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [all] Error 1
make[1]: *** [all] Error 2
make: *** [utils] Error 2


 

Hiram Clawson <hiram <at> soe.ucsc.edu> May 09 04:00PM -0700  

Good Afternoon Grant:
 
Please correct the 'makefile' in the bigBedNamedItems
directory to read:
 
kentSrc = ../..
A = bigBedNamedItems
include $(kentSrc)/inc/userApp.mk
L += -lm -lz
 
Your 'makefile' is probably missing the -lz on the L += line.
It was updated after the most recent source code release.
 
--Hiram
 
On 5/9/13 3:03 PM, grant hartzog wrote:


 

Pauline Fujita <pauline <at> soe.ucsc.edu> May 09 12:42PM -0700  

Hello Hongxin,
 
Unfortunately this is beyond the scope of this mailing list - which
is to address specific questions about the UCSC Genome Browser
software, database, genome assemblies and release cycles.
 
You might want to consult the "support" section of the GMOD site:
 
http://gmod.org/wiki/Main_Page
 
 
Best of luck with your research,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 
On Thu, May 9, 2013 at 8:04 AM, Zhang, Hongxin (MU-Student)


 

Pauline Fujita <pauline <at> soe.ucsc.edu> May 09 12:29PM -0700  

Hello Ruti,
 
You can use our liftover tool to convert coordinates between
assemblies. You will find the tool here:
 
https://genome.ucsc.edu/cgi-bin/hgLiftOver
 
(also accessible by clicking the "utilities" menu on the left,
followed by the "batch coordinate conversion" link)
 
Note that your coordinates will need to be in BED or chrN:start-end
(i.e. chr18:43484054-72498703) formats. For more info on BED format
see this help doc: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
 
If you are looking at a coordinate within a browser (i.e. you're
looking at Chr18:43,484,054-72,498,703 in the hg18 browser) you can
also jump to the corresponding location in another browser - i.e. hg19
by clicking on the "View" menu in the top bar, and selecting "In Other
Genomes (Convert)"
 
If you have further questions please feel free to contact the mailing
list again at genome <at> soe.ucsc.edu.
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• Greetings - Help Please! Paul Freiman [1 Update]

Pauline Fujita <pauline <at> soe.ucsc.edu> May 03 04:52PM -0700  

Hello Paul,
 
You might find this tutorial on the Genome Browser to be a useful
starting point:
 
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=27
 
In response to your specific questions:
 
1) The first position of a chromosome in the Genome Browser is 1. To
see it, navigate to the beginning of a chromsome (chr1:1-20, for
instance) and look at how the bases are numbered. Note that in our
tables, though, the first base is numbered 0. See this page to read
about why: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms.
 
2) Ns take up space, just as A, C, G, and T do.
 
3) Masking does not affect positioning.
 
Hopefully this is enough to get you started. If you have further
questions please feel free to contact the mailing list again at
genome <at> soe.ucsc.edu.
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• Searching for BACs [1 Update]
• Removing custom tracks [3 Updates]
• NOR regions on chr13,14,15,21,22 [1 Update]

Michael Krahn <krahnmichael <at> hotmail.com> May 03 03:32PM +0200  

Hi!
I would like to search for a specific BAC for my gene of interest - I remember, that this was possible in the genome viewer, however I cannot find out how.
Many thanks for your help !
Michael


 

Brooke Rhead <rhead <at> soe.ucsc.edu> May 02 12:15PM -0700  

Hi Brad,
 
I spoke to our developers, and there aren't any straightforward ways to
find the custom track number. There might be an easier way to
accomplish your goal, though. You could potentially use a track hub
instead, which would allow you to control the contents of the hub and
make changes to it without interacting with the Genome Browser at all
(see http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html for more
info). Alternatively, perhaps you could use a saved session
(http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html); for
instance, we have an FAQ that describes how to link to specific tracks
in the Genome Browser using a saved session with all tracks hidden:
http://genome.ucsc.edu/FAQ/FAQlink.html#link4.
 
What is your usage scenario? Maybe we can suggest some alternatives.
 
--
Brooke Rhead
UCSC Genome Bioinformatics Group
 
 
On 5/1/13 3:57 PM, Brad Davis wrote:


 

Brad Davis <bdavis <at> bcgsc.ca> May 02 12:28PM -0700  

Hello Brooke,
 
We are building an epigenome portal to allow users to view the reference
epigenomes being created at the BC Cancer Agency. It is similar in function
to the Epigenome Roadmap Atlas. Currently when a user selects a set tracks
they want to visualize the track information is written to a hub file at a
internet accessible address and this hub file (e.g.
http://edccwashu.bcgsc.ca/hubs/hub.ucsc.Thu-May--2-04-27-39-2013.wmS5iRPtf0)
is then transmitted as part of the HTTP request to the UCSC browser. The
issue is that if a user selects a track decides to visualize it and then
comes back to the table and unselects a track, the track continues to be
displayed on the genome browser. I understand that the user can remove the
track from their display using the manage tracks feature of the UCSC
browser, but I was hoping to make our table a little bit more transparent to
for users. The manage tracks tool is great, but I am aiming to make as few
assumptions about the users understanding of genome browsers as possible.
Admittedly any experienced user will be familiar with them, but I would like
to not have to make that assumption. I know that there is a feature which
allows for all of the tracks to be removed as a group, but that goes too
far. I can imagine a scenario where a user has loaded their own tracks
manually (or via some other genomics data center) and then comes to ours to
load tracks. If we automatically cleared the track history for them every
time they selected a track it would undo any previous work they had done, so
the remove all tracks feature really isn't an option. The TrackHub
suggestion might work, I'll have to talk with our guys, but it seems like a
promising solution. Ideally what we want is something that we can integrate
into our current system.
 
Thanks,
Brad Davis
 


 

Brooke Rhead <rhead <at> soe.ucsc.edu> May 02 05:42PM -0700  

Hi Brad,
 
We don't currently have a mechanism in track hubs or in custom tracks to
control visibilities of data hubs, or a way to disconnect from a
particular hub via URL, so on second thought, track hubs might not be
the best solution for now.
 
Instead, you may be able to get to the custom track table names with the
numbers appended to them by constructing a URL to the Table Browser and
then doing some screen scraping. For instance, this URL will take you
to the Table Browser for hg19 with the Custom Tracks track group selected:
 
http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=user
 
You might have to do some experimenting to make it work.
 
--
Brooke Rhead
UCSC Genome Bioinformatics Group
 
 
On 5/2/13 12:28 PM, Brad Davis wrote:


 

Andrew Fritz <ajfritz <at> buffalo.edu> May 02 03:46PM -0400  

Hi,
I am trying to find the exact base pair beginning and end sites for the
nucleolar organizing regions on chromosomes 13,14,15,21,and 22, but I cant
seem to find this information anywhere. All I know is that they are on the
p arms of these chromosomes but I need to know much more specifically.
Thank you!
Andrew Fritz
University at Buffalo


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• Genome coordinate order [1 Update]
• ABOUT Mir1954 coordinate [1 Update]
• SFTP for bigwig/BAM custom tracks [2 Updates]

sjammula <sjammula <at> myriad.com> May 01 10:15AM -0600  

Hello,
 
In the past, I have seen the genome coordinates increase from left to right when any gene is displayed. But now I notice that the display shows them decreasing from from left to right.
 
Is there a way to change the display to go back to the old way of displaying coordinates ?
 
I use Safari on an imac to access genome browser.
 
Thanks,
Srikanth Jammulapati


 

Yabin Guo <Yabin.Guo <at> UTSouthwestern.edu> Apr 30 10:59PM  

To whom it may concern,
I'm search the info for Mir1954 (NR_035479) in the mouse genome. I found it in both your server and NCBI, but the coordinates are so different (see below). May you please explain this to me?
 
http://genome.ucsc.edu/cgi-bin/hgGene?hgsid=334773881&db=mm10&hgg_gene=uc029udz.1&hgg_chrom=chr2&hgg_start=113423522&hgg_end=113423560
 
http://www.ncbi.nlm.nih.gov/gene/?term=NR_035479
 
Thanks so much.
Best,
Yabin
 
UTSW Mol. Biol.
 
________________________________
 
UT Southwestern Medical Center
The future of medicine, today.


 

Michael Mueller <michael.mueller <at> imperial.ac.uk> Apr 30 10:07PM +0100  

Hi,
 
I was wondering if there is a way of getting bigwig/BAM tracks to work
with SFTP connections?
 
Michael


 

Brian Lee <brianlee <at> soe.ucsc.edu> Apr 30 03:03PM -0700  

Dear Michael,
 
Thank you for using the UCSC Genome Browser and your question about using
SFTP for bigWig and BAM custom tracks.
 
Unfortunately SFTP connections are not currently supported, we may support
them in the future and your interest in such a feature has been noted. We
do support FTP, HTTP, and HTTPS. For HTTPS connections passwords need
hexidecimal representation. For example, in the password mypwd at wk, the <at>
character should be replaced by %40, resulting in the modified password
mypwd%40wk.
 
Thank you again for your inquiry and using the UCSC Genome Browser. If you
have further questions, please feel free to contact the mailing list again
at genome <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genome Bioinformatics Group
 
 
On Tue, Apr 30, 2013 at 2:07 PM, Michael Mueller <


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• want to get the sequence from my selected region [1 Update]
• How to get SNP information. [1 Update]
• canFam3 SNPs [1 Update]
• Exon numbering convention followed by UCSC [1 Update]

Moonmoon Deb <moonmoondeb <at> gmail.com> Apr 26 06:07PM +0530  

sir
please let me know how can i download the sequence of my selected region of
a chromosome
--
Thanking You with Regards.
Moonmoon Deb


 

Pauline Fujita <pauline <at> soe.ucsc.edu> Apr 25 04:31PM -0700  

Hello Venkat,
 
The best option for that number of gene regions would be to use the Table
Browser and the define regions function. To do this go to the Table Browser
(http://genome.ucsc.edu/cgi-bin/hgTables) and select:
 
group: Variation and Repeats
track: All SNPs (137)
table: snp137
 
region: click the "define regions" button
 
In the region definition menu, you can paste or upload a file containing
the coordinates of your gene regions of interest. These coordinates will
need to conform to the syntax used in the browser - which is described just
below the box where you can enter them.
 
Note also that our coordinates always have a zero-based start and a
one-based end - you can read more about that in this FAQ:
 
http://genome.ucsc.edu/FAQ/FAQtracks#tracks1
 
If you do not already know the coordinates of your regions of interest, you
could also generate a list of coordinates based on a list of genes using
the Table Browser. To do this select:
 
group: Genes and Gene Prediction Tracks
track: your preferred gene prediction track (i.e. UCSC Genes)
table: knownGene
 
region: genome
identifiers: click "paste list" and enter your list of gene names - note
that they will have to be of the form described by the examples
 
output format: BED
 
then after clicking 'get output' you will need to specify which genic
regions you want to include (i.e. intron/exons etc). You can then use this
BED output in the "define regions" step above.
 
If you have further questions please feel free to contact the mailing list
again at genome <at> soe.ucsc.edu.
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 
 
 
 
 


 

Mehar <mehar.com <at> gmail.com> Apr 25 11:05PM +0300  

Hi,
 
I am in need of known SNPs file for canFam3 build and I am regularly
looking at the link
_http://hgdownload.soe.ucsc.edu/goldenPath/canFam3/database/_ since 2011
september, to download the known SNPs file. Unfortunately, it was not
available in the canFam3 annotation database.
 
Could someone help to provide the SNP file for canFam3?
 
Thanks in advance.
 
 
Regards
Mehar


 

Pauline Fujita <pauline <at> soe.ucsc.edu> Apr 25 12:34PM -0700  

Hello Rohit,
 
This depends where you are looking at the exon numbers. For output from the
Table Browser (genome.ucsc.edu/cgi-bin/hgTables) exons will be numbered in
order of increasing chromosomal coordinate (not 5' to 3').
 
However, if you are looking at RefSeq in the browser, and have the
next/previous exon navigation arrows turned on (enabled by clicking on the
"configure" button below the main browser display - and checking the box at
the top), then the exon numbers you will see as you hover your mouse above
the next/prev arrow are numbered 5' to 3' to match RefSeq.
 
Hopefully this clarifies things. If you have further questions please feel
free to contact the mailing list again at genome <at> soe.ucsc.edu.
 
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 
 
 
On Thu, Apr 25, 2013 at 4:05 AM, Rohit Gavval <rohit_gavval <at> persistent.co.in


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• What program reads ".bb" TFBS file from ENCODE? [2 Updates]
• Normalized data for RNA-seq and Chip-seq data for differential analysis [1 Update]

David Nguyen <d.hh.nguyen <at> gmail.com> Apr 18 02:55PM -0400  

Hi there,
 
I'm interested in looking at the TFBS data and downloaded the files. One
is called:
 
spp.optimal.wgEncodeBroadHistoneGm12878CtcfStdAlnRep0_VS_wgEncodeBroadHistoneGm12878ControlStdAlnRep0
 
However, I don't have a program that can open this file.
What and where is the program for this?
 
Thanks,
 
-dave


 

Brian Lee <brianlee <at> soe.ucsc.edu> Apr 19 10:06AM -0700  

Dear Dave,
 
Thank you for using the UCSC Genome Browser and your question about ".bb"
files. Files ending in ".bb" are
bigBed<http://hgwdev.soe.ucsc.edu/FAQ/FAQformat.html#format1.5>
files.
 
Click this link, http://hgwdev.soe.ucsc.edu/goldenPath/help/bigBed.html, for
extensive information on the bigBed format and how to extract data with
different binary utilities located in this
directory<http://hgdownload.cse.ucsc.edu/admin/exe/>
: http://hgdownload.cse.ucsc.edu/admin/exe/
 
Thank you again for your inquiry and using the UCSC Genome Browser. If you
have further questions, please feel free to contact the mailing list again
at genome <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genome Bioinformatics Group
 


 

xiewanchen2013 <xiewanchen2013 <at> gmail.com> Apr 19 10:14PM +0800  

Dear Madam/Sir,
 
I want to know if there is any available data of normalized RNA-seq and Chip-seq data for differential analysis between cell-lines such as by edgeR or DEseq.
 
Thank you for your time!
 
 
 
 
xiewanchen2013


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• Scan Regions [2 Updates]
• slow download for ENCODE [1 Update]

Meenakshi Sharma <meenakshi8 <at> gmail.com> Apr 14 10:28PM -0500  

Hello,
 
I have a question. Suppose I have genomic regions (with start and
end locations) from human genome. And I want to know whether these regions
are part of genes or repetitive elements. I am interested in biological
function of these regions.
 
Is there a combined general database which I can use to query these regions
against?
Currently I scan these regions against refGene db.
 
Thanks and regards,
Meenakshi Sharma


 

Hiram Clawson <hiram <at> soe.ucsc.edu> Apr 15 08:08AM -0700  

Good Morning Meenakshi:
 
The UCSC genome browser would be an appropriate tool
for this exploration.
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
 
You construct a custom track of your regions of interest,
then intersect gene tracks or the repeat masking track
with your custom track.
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
 
--Hiram
 
On 4/14/13 8:28 PM, Meenakshi Sharma wrote:


 

"Rosenfeld, Jeffrey" <rosenfj1 <at> umdnj.edu> Apr 13 09:11PM -0400  

Hi,
 
Is there a mirror for the ENCODE data? The download is extremely slow.
 
Thanks,
 
Jeff
 
------------------------------------------------------
Jeffrey Rosenfeld, Ph. D
IST/High Performance and Research Computing
University of Medicine and Dentistry of New Jersey (UMDNJ)
973-972-1004 (voice)
973-972-7412 (fax)
MSB-C631
185 South Orange Avenue
Newark, NJ 07101
 
Sackler Institute for Comparative Genomics
American Museum of Natural History


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• Problem displaying custom tracks [1 Update]
• SNP tracks [1 Update]

Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Apr 12 01:21PM -0700  

Hi Brad,
 
Your URL (http://www.bcgsc.ca/downloads/edcc/test/fib03_Standard.bed)
already contains a track line, which is why you are receiving this
error. Replace the second line of your customTracks.txt file with only
the URL, and it should upload without any errors.
 
If you have further questions please feel free to contact the mailing
list again at genome <at> soe.ucsc.edu.
 
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
On 4/12/2013 9:50 AM, Brad Davis wrote:


 

Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Apr 12 01:12PM -0700  

Hi Marco,
 
You can read more about the SNP track on its track description page.
This can be accessed by clicking on the gray bar to the left of the
track in the main display, or by clicking on the track title above its
pull down menu below the main display. See the SNP 137 track description
here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=19&g=snp137. This
should provide the answers to questions 1 and 3.
 
To answer the second part of question 1, it really depends on the
purpose of your analysis. You could use the "All SNP" track, but note
that it contains not only polymorphisms, but also rare SNPs, known
disease SNPs, and variants that are questionable because they map to
multiple locations in the genome.
 
For your last question, the usual reason for inconsistency between the
dbSNP website and ours is that they constantly update their web
database, while we only load our SNPs tracks once when they make
official release download files.
 
I hope this helps. If you have additional questions, feel free to
contact us again at genome <at> soe.ucsc.edu.
 
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
On 4/12/2013 3:25 AM, Marco Santagostino wrote:


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• how to get dbSNP 137? [2 Updates]
• Why one protein appears more once in ucsc knownGene? And why some UniProt proteins are missing in knownGene? [1 Update]
• Custom Track URL error [1 Update]
• Falty refseq table download for hg19 [1 Update]
• error loading custom tracks [1 Update]
• To plot broadpeak signal in R [1 Update]
• acquiring a .2bit version of the starlet sea anemone genome [1 Update]
• how to search for ChIP_seq info [1 Update]
• interpretation of experimental scores wgEncodeRegTfbsClusteredV2 [1 Update]
• generating exon alignments [1 Update]
• Retrieving chromosomal loci from list of genes? [1 Update]

chenjh <chenjhbio <at> 163.com> Apr 05 04:24PM +0800  

dear sir,
Very sorry to trouble you.
 
 
But we met problems,would you like to tell us how to download human dbSNP 137?
 
 
many thanks for that in advance


 

Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Apr 05 09:50AM -0700  

Hello,
 
You can download dbSNP 137 tables directly from our downloads server.
From the main page, click on 'Downloads' (located on left-side
navigation menu). On the following page, click on 'Human' then
'Annotation Database'. This will take you here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/. Scroll down
and you will find all download files associated with dbSNP 137.
 
Please contact us again at genome <at> soe.ucsc.edu if you have any further
questions.
 
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
 
On 4/5/2013 1:24 AM, chenjh wrote:


 

Peng Yu <pengyu.ut <at> gmail.com> Apr 05 11:31AM -0500  

Hi,
 
The following mysql code shows that many proteins appears more than
once in knownGene.
 
~~~
mysql> select count(*) from knownGene where proteinID!="";
+----------+
| count(*) |
+----------+
| 41735 |
+----------+
1 row in set (0.32 sec)
 
mysql> select count(distinct proteinID) from knownGene where proteinID!="";
+---------------------------+
| count(distinct proteinID) |
+---------------------------+
| 34117 |
+---------------------------+
1 row in set (0.23 sec)
 
mysql> select proteinID from knownGene group by proteinID having
count(*) >=2 limit 5;
+-----------+
| proteinID |
+-----------+
| |
| A0ELI5 |
| A0JNT0 |
| A0JNY8 |
| A0JNZ2 |
+-----------+
5 rows in set (0.26 sec)
mysql> select * from knownGene where proteinID="A0ELI5";
+------------+-------+--------+----------+----------+----------+----------+-----------+-----------------------------------------------------------------+-----------------------------------------------------------------+-----------+------------+
| name | chrom | strand | txStart | txEnd | cdsStart |
cdsEnd | exonCount | exonStarts
| exonEnds
| proteinID | alignID |
+------------+-------+--------+----------+----------+----------+----------+-----------+-----------------------------------------------------------------+-----------------------------------------------------------------+-----------+------------+
| uc009pvp.1 | chr9 | + | 57556375 | 57597969 | 57561204 |
57596302 | 7 |
57556375,57561187,57563754,57574992,57587696,57592391,57595967, |
57556506,57561368,57564074,57575328,57587850,57592609,57597969, |
A0ELI5 | uc009pvp.1 |
| uc009pvq.1 | chr9 | + | 57556375 | 57597969 | 57575057 |
57596302 | 6 |
57556375,57561187,57574992,57587696,57592391,57595967, |
57556506,57561368,57575328,57587850,57592609,57597969, |
A0ELI5 | uc009pvq.1 |
+------------+-------+--------+----------+----------+----------+----------+-----------+-----------------------------------------------------------------+-----------------------------------------------------------------+-----------+------------+
2 rows in set (0.07 sec)
~~~
 
The following shows that UniProt has more mouse proteins than the ones
in knownGene.
~~~
~$ wget -qO- ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomes/MOUSE.fasta.gz
| gunzip | grep '^>' | wc -l
50798
~~~
 
Does anybody know why for both these questions?
 
--
Regards,
Peng


 

"Steve Heitner" <steve <at> soe.ucsc.edu> Apr 05 08:19AM -0700  

Hello, Shijian.
 
If you are unable to solve the connection problem at your institution, you
may consider one of the many public storage solutions available. Also, we
recommend using HTTP rather than FTP. The URL will operate more
efficiently, requiring only one connection and a single request rather than
two connections and several setup requests.
 
Please contact us again at genome <at> soe.ucsc.edu if you have any further
questions.
 
---
Steve Heitner
UCSC Genome Bioinformatics Group
 

 
From: genome <at> soe.ucsc.edu [mailto:genome <at> soe.ucsc.edu] On Behalf Of Zhangsj
Sent: Monday, April 01, 2013 4:39 PM
To: genome
Subject: Re:RE: [genome] Custom Track URL error
 

 
Sorry, I should had told that I had tried this and I really could view my
data on browser and I don't set the listen_address for vsftp. So I guess
it's not the IP permit for UCSC to access my FTP.
 

 

 
------------------ Original ------------------
 
From: "Steve Heitner"<steve <at> soe.ucsc.edu>;
 
Date: Tue, Apr 2, 2013 01:59 AM
 
To: "'Zhangsj'"<zhangsjsky <at> foxmail.com>; "'genome'"<genome <at> soe.ucsc.edu>;
 
Subject: RE: [genome] Custom Track URL error
 

 
Hello, Shijian.
 
I just attempted to browse to your FTP site and it was unavailable. If you
are unable to view the contents of the directory in a web browser, you will
likewise be unable to load your files as a custom track. Make sure that
when you browse to ftp://162.105.138.90, you can see your files in the
directory. Once you can do that, try loading your custom track again.
 
Please contact us again at genome <at> soe.ucsc.edu if you have any further
questions.
 
---
Steve Heitner
UCSC Genome Bioinformatics Group
 

 
From: genome <at> soe.ucsc.edu [mailto:genome <at> soe.ucsc.edu] On Behalf Of Zhangsj
Sent: Monday, April 01, 2013 8:39 AM
To: genome
Subject: [genome] Custom Track URL error
 

 
Hi, dear UCSC members
 

 
I want to upload BAM file to UCSC, but got the following error:
 
Can't access My BAM's bigDataUrl ftp://162.105.138.90/adipose.sorted.bam
and/or the associated index file
ftp://162.105.138.90/adipose.sorted.bam.bai: TCP non-blocking connect() to
162.105.138.90 timed-out in select() after 10000 milliseconds - Cancelling!
 

 
The track line is: track type=bam name="My BAM"
bigDataUrl=ftp://162.105.138.90/adipose.sorted.bam
 

 
I had set up FTP server on 162.105.138.90 with vsFTP and config it as
passive connection mode as UCSC requires. The anonymous FTP is on. The
adipose.sorted.bam.bai has been in the same directory as adipose.sorted.bam.
 

 
Did I miss something else? Hope your reply.
 

 
------------------
 
With best wishes,
 
Shijian Sky Zhang
 
---------------------------------------
Institute of Molecular Medicine, Peking University
Yingjie Exchange Center
Beijing 100871, China
E-mail: zhangsjsky <at> foxmail.com
 
zhangsjsky <at> pku.edu.cn
 

 
--



 
--


 

Pauline Fujita <pauline <at> soe.ucsc.edu> Apr 04 05:13PM -0700  

Hello Mark,
 
We think we might have corrected the issue. If you are still having
trouble with this please contact the mailing list again at
genome <at> soe.ucsc.edu.
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 
 


 

Pauline Fujita <pauline <at> soe.ucsc.edu> Apr 04 02:15PM -0700  

Hello Mary,
 
You may these help docs useful:
 
https://genome.ucsc.edu/goldenPath/help/customTrack.html
https://genome.ucsc.edu/goldenPath/help/wiggle.html
 
Note that all custom tracks must begin with a track line - as described here:
 
https://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK
 
Judging by the error you are seeing it looks like your custom track(s)
are missing a track line.
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 
 


 

Pauline Fujita <pauline <at> soe.ucsc.edu> Apr 04 01:51PM -0700  

Hello Herty,
 
If you are wanting to draw graphs of signal data from ENCODE, you probably
want to use the ENCODE uniform signals which are in bigWig format. These
are available from the ENCODE downloads page:
 
encodeproject.org/ENCODE/downloads.html
 
You may also find our documentation on ENCODE file formats useful:
 
http://encodeproject.org/FAQ/FAQformat.html#ENCODE
 
As far as R packages are concerned, unfortunately that is beyond the scope
of this list. There are quite a few packages available online, you will
have to see which best fits your needs. A good starting point might be the
bioconductor site:
 
http://www.bioconductor.org/help/search/index.html?q=R
 
Best of luck with your research! If you have further questions regarding
Genome Browser usage, please feel free to contact the mailing list again at
genome <at> soe.ucsc.edu.
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 
On Thu, Apr 4, 2013 at 2:45 AM, Herty LIANY (GIS)


 

Pauline Fujita <pauline <at> soe.ucsc.edu> Apr 04 01:25PM -0700  

Hello Sarah,
 
You can find the files you're look for in the downloads area of our test site:
 
http://hgdownload-test.soe.ucsc.edu/goldenPath/nemVec1/bigZips/
 
Note that in general, items on our test server have not been through
our quality assurance process and are subject to change.
 
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 


 

Kate Rosenbloom <kate <at> soe.ucsc.edu> Apr 04 12:59PM -0700  

Hello Brenden,
 
The Txn Factor ChIP-seq browser track contains clusters of enriched
sites from ChIP-seq performed in cell types from
all 3 tiers of ENCODE. You can see the complete list of cell types
included in this track on the track description page:
 
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV2
 
The table you pulled from the Table Browser includes information for
each cluster indicating which cell types contributed to the cluster, and
what the signal strength for that cell type was in the peak contributing
to the cluster, but not the specific coordinates for the peaks on a
cell-specific basis. For that, you would need the individual
per-cell-type datasets. The uniform ChIP-seq peaks that were used to
generate this version of the Txn Factor ChIP track are available at the
ENCODE Analysis Track Hub, for downloads, and access with the Table
Browser (and Genome Browser). For a limited number of datasets, you can
readily extract the peak coordinates for your region of interest using
the Table Browser after loading the track hub. You can do this directly
from the browser Track Connect page, or indirectly from the ENCODE
downloads page (click the TFBS link in the Uniform Peaks section
header): http://encodeproject.org/ENCODE/downloads.html
 
Unfortunately the ENCODE data is so voluminous that often downloading
the files and processing at your site is necessary to extract data for
your specific needs. To extract all ChIP-seq peaks in your region of
interest from the 400+ datasets represented here, you would need to
download the TFBS Peaks (SPP) via the download link, and filter the
resulting narrowPeak BED files for your regions of interest.
Fortunately the Peak files are the most compact of the ENCODE files, so
should be relatively easy to download.
 
Note that the datasets represented here are based on data submitted for
the ENCODE January 2011 data freeze, with analysis reported by the
ENCODE Analysis Working Group in coordinated publications in September
2012: http://encodeproject.org/ENCODE/analysis.html.
 
Cheers,
Kate
---
Kate Rosenbloom
UCSC Genome Bioinformatics
 
On 4/4/13 8:32 AM, Chen, Brenden wrote:


 

Brooke Rhead <rhead <at> soe.ucsc.edu> Apr 04 12:18PM -0700  

Hi Bob,
 
Input signal values are multiplied by a normalization factor calculated
as the ratio of the maximum score value (1000) to the signal value at 1
standard deviation from the mean, with values exceeding 1000 capped at
1000. This has the effect of distributing scores up to mean + 1std
across the score range, but assigning all above to the max score.
 
We are not aware of a standard threshold for weak interactions.
 
If you have further questions, please feel free to contact us again at
genome <at> soe.ucsc.edu.
 
--
Brooke Rhead
UCSC Genome Bioinformatics Group
 
 
On 4/2/13 3:58 PM, Robert O'Connor wrote:


 

Brooke Rhead <rhead <at> soe.ucsc.edu> Apr 04 12:00PM -0700  

Hi Navin,
 
If you are using the Table Browser to and the "CDS FASTA" output format,
then the CDS alignments from the UCSC Genes track (table: knownGene) are
in phase. If you are using RefSeq Genes (table: refGene), a few of the
refGene exons might not be in phase after the first exon since the mRNA
may have bases in it that aren't in the reference sequence, but the huge
majority will be in phase.
 
--
Brooke Rhead
UCSC Genome Bioinformatics Group
 
 
On 4/3/13 12:15 PM, Navin Rustagi wrote:


 

Brian Lee <brianlee <at> soe.ucsc.edu> Apr 04 11:47AM -0700  

Dear Mark,
 
Thank you for using the UCSC Genome Browser and your question about
obtaining chromosomal location of genes from unique identifiers such
as UCSC transcripts and Entrez Gene accession numbers.
 
You can use our Table Browser "identifiers (names/accessions):"
function to upload a list of genes and select the desired output from
the corresponding track. For example, you can pull the coordinates
from the UCSC genes knownGene table if you upload a file of UCSC gene
names similar to this:
uc007aet.1
uc007aeu.1
uc007aev.1
...
 
1. Navigate to the Table Browser Tool,
http://genome.ucsc.edu/cgi-bin/hgTables, and make the following
selections:
 
Clade: Mammal
Genome: Mouse
Assembly: mm9
Group: Genes and Gene Prediction Tracks
Track: UCSC Genes
Table: knownGene
Region: genome
 
2. Click the "upload list" button to use your UCSC genes identifiers
file in the format described above.
 
3. Set "output format:" to "selected fields from primary and related
tables" and click "get output".
 
4. On the "Select Fields from mm9.knownGene" page, select your desired
information. For example you can select "name", "chrom", "txStart",
and "txEnd" and then click "get output" to get information similar to
this:
 
#name chrom txStart txEnd
uc007aet.1 chr1 3195984 3205713
uc007aeu.1 chr1 3204562 3661579
uc007aev.1 chr1 3638391 3648985
...
 
If you have Entrez Gene identifiers of the type like "382301", which
corresponds to UCSC identifier "uc009vfk.1", you can get the same
output using the Table Browser "filter" tool.
 
1. Repeat step 1 above.
 
2. Click the "clear list" button to remove the previous identifier
operation. Next to "filter:", click the "create" button.
 
3. Scroll down to the "Linked Tables" section and put a check mark
next to the "knownToLocusLink" table and click the "allow filtering
using fields in checked tables" button.
 
4. Under "mm9.knownToLocusLink based filters", find the "values does
match" line. Replace the "*", with a list of your Entrez Gene
identifiers, for example paste, "18019 11735 11496 16709 12916 ..."
The box is small, but it will accept a list of identifiers.
 
5. Repeat step 3 from above.
 
6. Repeat step 4 from above. Here you could use the "Linked Tables" to
add the "value" from knownToLocusLink in your output and you will get
output like:
#mm9.knownGene.name mm9.knownGene.chrom mm9.knownGene.txStart
mm9.knownGene.txEnd mm9.knownToLocusLink.value
uc008oav.1 chr2 168301909 168415848 18019
 
When selecting a table to browse in the Table Browser, by clicking the
"describe table schema" button you can learn more about other tables.
For example you can also change the above examples Table Browser
settings to "Track: RefSeq Genes" and "Table: RefGene", if you are
using identifiers like "NM_001195025". Or you can make similar filter
selections using Linked Tables based on RefSeq's RefGene table rather
than UCSC knownGene to obtain RefSeq coordinate output. For example
linking through "knownToRefSeq" and then "knownToLocusLink" you can
filter on Entrez Gene IDs and select output like:
#mm9.refGene.name mm9.refGene.chrom mm9.refGene.txStart
mm9.refGene.txEnd mm9.knownToLocusLink.value
NM_010899 chr2 168301909 168415783 18019
 
Unfortunately it looks like we do not have any track or tables that
contain MGI identifiers of the type "MGI:1341105"
 
Thank you again for your inquiry and using the UCSC Genome Browser. If
you have further questions please feel free to contact the mailing
list again at genome <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genome Bioinformatics Group
 


 

Group: http://groups.google.com/a/soe.ucsc.edu/group/genome/topics

• different IQCF1 region between UCSC and Ensembl [1 Update]
• Question about mRNA identifier name [1 Update]
• affymetrix probeset track info [1 Update]

Luvina Guruvadoo <luvina <at> soe.ucsc.edu> Mar 22 03:14PM -0700  

Hi Chen,
 
There are actually two UCSC gene models for IQCF5:
 
uc003dbq.4 chr3:51,840,728-51,937,386 (which matches Ensembl)
uc011bdx.2 chr3:51,907,737-51,909,600
 
Note, the transcript you are referred to in your email corresponds to
IQCF5. You can read more about how UCSC genes are built on the track
description page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene
 
If you have further questions please feel free to contact the mailing
list again at genome <at> soe.ucsc.edu.
 
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
On 3/22/2013 9:27 AM, mingchen wrote:


 

Pauline Fujita <pauline <at> soe.ucsc.edu> Mar 22 12:12PM -0700  

Hello Ganesh,
 
uc010dhl.1 is the unique identifier given to this transcript variant
within the "UCSC genes" gene prediction dataset. These identifiers are
generated when we create this track here at UCSC, and updated if the
transcript changes. You can read more about the UCSC genes track on
its description page here:
 
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene
 
Hopefully that is enough to get you started. If you have further
questions please feel free to contact the mailing list again at
genome <at> soe.ucsc.edu.
 
Best regards,
 
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
 
 
 


 

Brooke Rhead <rhead <at> soe.ucsc.edu> Mar 22 11:47AM -0700  

Hi Matt,
 
I see now. The links from Affymetrix load four custom tracks into the
Genome Browser (they show up in the track controls under the group
"other" at the bottom of the page). You will need to contact Affy
directly about the contents of the tracks, since we don't actually host
the data here.
 
--
Brooke Rhead
UCSC Genome Bioinformatics Group
 
 
On 3/22/13 2:32 AM, matt arno wrote: