genome | 17 Feb 18:23 2015

Digest for genome <at> soe.ucsc.edu - 1 update in 1 topic

Brian Lee <brianlee <at> soe.ucsc.edu>: Feb 16 11:00AM -0800

Dear Penny,
 
Thank you for using the UCSC Genome Browser and your question about
netClass usage.
 
The tDb and qDb items, where you have entered maskt and maskq, are meant to
represent MySQL databases that should exist in a MySQL server. What you
have entered, maskt and maskq, do not exist, explaining the error you are
seeing, "Unknown database 'maskt'.
 
In the example on the wikipage (momentarily unavailable), netClass -noAr
noClass.net ci2 cioSav2 cioSav2.net, the "ci2" and "cioSav2" represent two
assemblies that netClass accesses on a MySQL server.
 
To see more about using the public access MySQL database, and adding a
.hg.conf file, see this page:
http://genome.ucsc.edu/goldenPath/help/mysql.html Example usage: mysql
--user=genome --host=genome-mysql.cse.ucsc.edu -A -Ne 'show tables' ci2;
 
It may be helpful to note that the cioSav2 assembly, in the above example,
is one that has been added to the development MySQL environment,
http://genome-preview.ucsc.edu/cgi-bin/hgTracks?db=cioSav2, but is not
available from the Public MySQL server.
 
We have mailing list archives where people using netClass have asked
questions that may have helpful answers for your situation. Please review
this answer and search the google group archive for similar questions
before mailing the list again:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/BYb35wDEwKI/-PKU8C9VI_MJ
 
Note the information in the above previous answer regarding If you are
aligning assemblies that are not hosted by UCSC, that you could set up your
own MySQL server and put information for accessing it into a .hg.conf file
in your home directory, or skip this netClass step of the alignment process.
 
Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please first search the google group archive
for similar questions before mailing the list at genome <at> 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-www <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genome Bioinformatics Group
 
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genome | 16 Feb 18:26 2015

Digest for genome <at> soe.ucsc.edu - 1 update in 1 topic

"淚鱼" <liang_ping_ping <at> 163.com>: Feb 15 02:07PM +0800

dear,I have a problem about netClass when I doing Whole genome alignment
http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto‍).Can you help me?
---penny
 
 

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genome | 14 Feb 18:08 2015

Digest for genome <at> soe.ucsc.edu - 5 updates in 2 topics

"seirana.hashemi" <seirana.hashemi <at> ut.ac.ir>: Feb 13 11:16PM +0330

Hello,
 
Dear Sir/Madam,
 
I Emailed you before to ask some question about GRCh37, your answers
were very useful,and I really appreciate. In the continue I have some
other questions:
 
There are txStart and txEnd columns in UCSC Genes track, knownGene
table. what are these? also there are cdsStart and cdsEnd; are they
abbreviations for "start of coding regions" and "end of coding regions"?
and another question is: how can align minus strand to plus strand,
because I have to work only on plus strand. Is it correct? chromosome
size - txStart in minus strand = txStart in plus strand?
 
Looking forward to receiving your kind reply at your earliest
convenience
 
Yours sincerely,
Seirana Hashemi
"Steve Heitner" <steve <at> soe.ucsc.edu>: Feb 13 02:43PM -0800

Hello, Seirana.
 
Thank you for your kind words. We certainly always try to be as helpful as possible. :)
 
The txStart and txEnd fields indicate the start and end of transcription, which includes both coding and non-coding regions. As you properly identified, the cdsStart and cdsEnd fields indicate the start and end of the coding regions only.
 
Note that even transcripts on the - strand have their txStart, txEnd, cdsStart and cdsEnd fields defined in terms of the + strand. If your goal is to get everything in terms of + strand coordinates, then most of the work is already done for you. The only important thing to understand is that because everything is defined in terms of the + strand, what we list as txStart for - strand items is actually the end of transcription and what we list as txEnd for - strand items is actually the start of transcription. It is organized in this manner for purposes of drawing the items in our display.
 
Please contact us again at genome <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-www <at> soe.ucsc.edu.
 
---
Steve Heitner
UCSC Genome Bioinformatics Group
 

 
From: seirana.hashemi [mailto:seirana.hashemi <at> ut.ac.ir]
Sent: Friday, February 13, 2015 11:46 AM
To: genome <at> soe.ucsc.edu
Subject: [genome] some questions about UCSC Genes track, knownGene table
 

 
Hello,
 
Dear Sir/Madam,
 
I Emailed you before to ask some question about GRCh37, your answers were very useful,and I really appreciate. In the continue I have some other questions:
 
There are txStart and txEnd columns in UCSC Genes track, knownGene table. what are these? also there are cdsStart and cdsEnd; are they abbreviations for "start of coding regions" and "end of coding regions"? and another question is: how can align minus strand to plus strand, because I have to work only on plus strand. Is it correct? chromosome size - txStart in minus strand = txStart in plus strand?
 
Looking forward to receiving your kind reply at your earliest convenience
 
Yours sincerely,
 
Seirana Hashemi
 
--
"Steve Heitner" <steve <at> soe.ucsc.edu>: Feb 13 10:02AM -0800

Hello, Bogdan.
 
A very similar question was asked recently. Please see https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/IEP_aZjQp_s/-XB_nPwWcEMJ. You can also view the schema of the RepeatMasker track by viewing the track description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19 <http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=rmsk> &g=rmsk) and clicking the “View table schema” link.
 
I believe your question about the reference sequences of transposons that the program uses would be best directed to the folks at RepeatMasker.
 
Please contact us again at genome <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-www <at> soe.ucsc.edu.
 
---
Steve Heitner
UCSC Genome Bioinformatics Group
 

 
From: Bogdan Tanasa [mailto:tanasa <at> gmail.com]
Sent: Thursday, February 12, 2015 10:26 PM
To: genome <at> soe.ucsc.edu
Subject: [genome] about RepeatMasker
 

 
Dear all,
 
please could you advise about the coordinates repStart, repEnd and repLeft in the output of RepeatMasker, and about the Reference Sequences of Retrotransposons that the program uses. thank you,
 
-- bogdan
 
--
Bogdan Tanasa <tanasa <at> gmail.com>: Feb 13 10:10AM -0800

Hi Steve,
 
thank you for your reply. If I may add one more question, this is about the
the data from ENCODE or RoadMap Epigenomics :
are the latest tracks from ENCODE or Roadmap Epigenomics already available
in UCSC genome browser ? thanks, and happy weekend,
 
bogdan
 
Brian Lee <brianlee <at> soe.ucsc.edu>: Feb 13 10:45AM -0800

Dear Bogdan,
 
Thank you for your question about the latest tracks from ENCODE or Roadmap
Epigenomics. For the latest information from both these sources you should
contact them directly.
 
At UCSC, only ENCODE data from 2003 to 2012, capturing the pilot project
and previous “ENCODE2” phase, are accessible currently. See the top of our
ENCODE page, http://genome.ucsc.edu/ENCODE/, for more information.
 
The new ENCODE portal, https://www.encodeproject.org, includes any new data
produced from 2013 to present day, as well as all publicly available ENCODE
data. For ENCODE data questions, please contact the ENCODE portal at
encode-help <at> lists.stanford.edu
 
At UCSC, for the Roadmap Epigenomics project, we feature two Public Hubs,
http://genome.ucsc.edu/cgi-bin/hgHubConnect, externally maintained and
updated by the Roadmap Project. You can find one hub for their Complete
Collection and a second Integrative Analysis Hub:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapIntegrative.txt
 
For all Roadmap Epiginomics data questions, please contact their website,
http://www.roadmapepigenomics.org/
 
In summary, you should send questions directly to ENCODE or the Roadmap
Epigenomics Group with any questions about their very latest information.
If you have any further UCSC questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genome Bioinformatics Group
 
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genome | 24 Jan 18:23 2015

Digest for genome <at> soe.ucsc.edu - 1 update in 1 topic

asma.mistadi <at> yahoo.com: Jan 23 05:59PM -0500

I am very interested in knowing several thing about UCSC genome browser like the following:
 
What is the biggest data set that was used in this genome browser? What is the size of it?
 
How many concurrent user can your genome browser handle??
 
How fast is the navigation and uploading functions?
 
How many tracks can be shown? Is there an upper limit?
 
Best Regards
Asma Mistadi
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genome | 23 Jan 18:07 2015

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Jan 23 09:04AM -0800

Hello Havard,
 
Thank you for your question. For each item in a BED file, the program
reports the highest and lowest scores that were found in the boundaries of
the BED item. However, if you are looking for maxima from overlapping
tiles, if this is what you mean by "the maximum found of every 10 bp tile
within this region", then you can use the -samplAroundCenter option. The
sampleAroundCenter=N option takes a sample of N bases around the center of
each BED item. To do this, your BED file should contain one entry for each
position like so:
 
chr17 1 2
chr17 2 3
chr17 3 4
chr17 4 5
 
Use -sampleAroundCenter=10. Note, it is integer arithmetic, so fractions
are truncated (4.5 is turned into 4).
 
Alternatively, you may be interested in bwtools from Andy Pohl which can
manage any kind of intersection with bigWig files:
https://github.com/CRG-Barcelona/bwtool
 
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
On Wed, Jan 21, 2015 at 2:24 AM, Håvard Aanes <Havard.Aanes <at> rr-research.no>
wrote:
 
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Jan 23 08:32AM -0800

Hello Rhianna,
 
Thank you for your question. You can read more about the CpG Islands track
and how it was constructed on the description page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cpgIslandSuper. A CpG
islands are regions with a high frequency of CG nucleotides which may or
may not have nearby transcription factor binding sites.
 
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
On Wed, Jan 21, 2015 at 8:32 AM, Sundsbak, Rhianna S. <
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genome | 22 Jan 18:21 2015

Digest for genome <at> soe.ucsc.edu - 4 updates in 4 topics

"Steve Heitner" <steve <at> soe.ucsc.edu>: Jan 22 09:09AM -0800

Hello, Beth.
 
Unfortunately, there is no way to feed Table Browser input into the output. Also, it is possible to create a custom track of your genomic coordinates and create an intersection with a gene track to overcome the 1,000-region limitation, but when doing that, it limits the output formats available and you no longer have the ability to select the fields you would like in your output. My best suggestion in this type of situation would be to break up your query by chromosome, but with over 200K regions, this would still give you an average of ~10K regions per chromosome which is still well over the limit.
 
Please contact us again at genome <at> soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-www <at> soe.ucsc.edu.
 
---
Steve Heitner
UCSC Genome Bioinformatics Group
 

 
From: Beth Marosy [mailto:bmarosy1 <at> jhmi.edu]
Sent: Friday, January 16, 2015 9:58 AM
To: genome <at> soe.ucsc.edu
Subject: [genome] How to annotate a list of regions
 

 
Hello UCSC,
 

 
I am trying to figure out how to upload a list a defined regions, and output a corresponding gene name/symbol to go with each region and need your help. I have tried to utilize the table browser, selecting the Gene/GenePredictions group, UCSC Genes track, and knownGene table. Then selecting define regions and pasting a list. Using the output format, I can select which fields I want to display in the output. However, when I get the output it doesn’t match the gene name to the input list, I only get the gene name. Is there a way to match the output to the input, so I know which gene goes to which defined region from the input?? Also, I have a very large list of regions that I need to do this with (207,000) – is there a way to do this with larger files?
 

 
Thanks for your help!!
 
 
Best,
Beth Marosy
 
--
"Steve Heitner" <steve <at> soe.ucsc.edu>: Jan 21 01:51PM -0800

Hello, Andrew.
 
We do not have any tracks that specifically deal with nucleolar organizer regions. It is also beyond the scope of this mailing list for us to speculate as to whether or not the NOR ends where the first BAC begins.
 
In addition, the following page indicates that the short arms of the relevant chromosomes do not exist on the current human assembly: https://www.iscb.org/cms_addon/conferences/ismb2014/posterlist.php?cat=G (see the second section down, Poster - G02). I verified in the Browser that on these particular chromosomes, no annotations exist in the short arm regions.
 
Please contact us again at genome <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-www <at> soe.ucsc.edu.
 
---
Steve Heitner
UCSC Genome Bioinformatics Group
 

 
From: Fritz, Andrew James [mailto:Andrew.Fritz <at> med.uvm.edu]
Sent: Friday, January 16, 2015 5:54 AM
To: genome <at> soe.ucsc.edu
Subject: [genome] NOR start and end sites
 

 
Hi,
I was just wondering if there is any information on the exact (or rough estimate) of where the nucleolar organizer regions (NOR) start and end on the acrocentric chromosomes (13,14,15,21, and 22). This information is of critical importance for the project I am planning and all I can find is where there are no longer any BACs or mRNA etc anymore on the chromosome. Is the first BAC likely to be the end of the NOR?
 

 
Thank you so much for your help,
 
 
Andrew Fritz, PhD.
 
Given E209
 
University of Vermont
 
Biochemistry Department
 
Burlington, VT 05401
 
(802) 656-4878
 
--
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Jan 21 11:47AM -0800

Hello Jeffrey,
 
Thank you for contacting us. One of our engineers provided the following
information:
 
FTP uses 2 TCP connections, command and data.
HTTP only needs to use one.
 
Passive FTP :
command : client >1023 -> server 21
data : client >1023 -> server >1023
 
Handy description of active and passive FTP:
http://slacksite.com/other/ftp.html
 
If you use ftp, your host will need to receive the command on port 21. If
you configure your FTP server, you can limit to a certain pre-allocated
port range and only let the firewall through for that set of ports, but you
need to make sure that you can support plenty of simultaneous connections,
as there can be multiple users for shared hubs and custom tracks. Even a
single user with many tracks turned on will generate multiple connections
being used.
 
Here are a couple of useful links for your reference:
 
Configuring FTP servers, covers ftp port range.
http://slacksite.com/other/ftp-appendix1.html
 
Configuring Firewall, covers ftp port range.
http://slacksite.com/other/ftp-appendix2.html
 
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
On Tue, Jan 20, 2015 at 5:02 PM, Alexander, Jeffrey <
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Jan 21 11:28AM -0800

Hello Nandita,
 
Thank you for your inquiry. You may now find this liftOver file available
for download here:
http://hgdownload.soe.ucsc.edu/goldenPath/dm6/liftOver/
 
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
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genome | 19 Jan 18:21 2015

Digest for genome <at> soe.ucsc.edu - 3 updates in 3 topics

Vidar Blikstad <vidar.blikstad <at> gmail.com>: Jan 17 03:38PM +0100

Hello
 
Is it possible to ask for help regarding a SQL query at the Table Browser?
(see attachment)
(I could forward a substatial donation to your institution)
 
 
 
Sincerely
Vidar Blikstad
Norway
Benoit Ballester <benoit.ballester <at> inserm.fr>: Jan 19 12:26PM +0100

Hi,
 
I am using the Genome Browser on a iMac with retina display, and the tracks (+fonts) appears blurry.
Do you have plans on supporting retina displays ? Or do you have a work around for this ?
 
Thanks for your advices,
 
Ben
--
Benoît Ballester, PhD
"Abraham J. Boyarsky" <abraham.boyarsky <at> concordia.ca>: Jan 18 08:20PM

Hello
 
I'm a mathematician in Canada with very little genomic knowledge. I am looking for human coding exon sequences of length about 1000. Can you please inform me how to find these on your website?
 
thank you
 
abraham boyarsky
professor of mathematics
concordia university
abraham.boyarsky <at> concordia.ca<mailto:abraham.boyarsky <at> concordia.ca>
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genome | 1 Jan 18:12 2015

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

"Oberdick, John" <oberdick.1 <at> osu.edu>: Dec 31 05:38PM

Hello. I am browsing the UCSC mouse genome and have one simple question. Are the indicated population frequencies of various SNPs based on single individuals from the reference genome strain (C57BL/6), or is it based on sequence data from individual mice of multiple strains? That is to say the SNP frequencies appear to be based on percentages out of 30 individuals (T: 33.333% (10 / 30); C: 66.667% (20 / 30)..., etc). But I cannot find any indication of the strain composition of the 30 mice.
 
My larger question is how much SNP variation would one expect to see amongst individuals within an inbred strain? I assume the answer is very little. Thanks for your help here. -John Oberdick
 
John Oberdick, Associate Professor
Department of Neuroscience
The Ohio State University Wexner Medical Center
Co-Director, Neuroscience Graduate Studies Program
The Ohio State University
206 Rightmire
1060 Carmack Rd
Columbus, OH 43210
P: 614-292-8714
Fax: 614-292-5379
oberdick.1 <at> osu.edu
CH Albach <calbach <at> google.com>: Dec 30 05:57PM -0800

73 NM_001282171 chr19_KI270922v1_alt + 92406 143045 92443 123738 9 92406,95658,97510,100973,123126,123693,123733,123844,143022, 92477,95958,97804,101024,123231,123731,123746,124394,143045, 0 KIR3DS1 cmpl cmpl 0,1,1,1,1,2,1,-1,-1,
73 NM_001282171 chr19_KI270923v1_alt + 93829 144461 93866 125161 9 93829,97078,98930,102393,124549,125116,125157,125267,144438, 93900,97378,99224,102444,124654,125155,125169,125817,144461, 0 KIR3DS1 cmpl cmpl 0,1,1,1,1,2,2,-1,-1,
73 NM_001282171 chr19_KI270929v1_alt + 90671 141314 90708 122029 9 90671,93923,95775,99239,121417,121984,122024,122135,141291, 90742,94223,96069,99290,121522,122022,122037,122685,141314, 0 KIR3DS1 cmpl cmpl 0,1,1,1,1,2,1,-1,-1,
608 NM_025259 chr6_GL000250v2_alt + 3090765 3095290 3090765 3095143 13 3090765,3091159,3091377,3091708,3092036,3092397,3092701,3093301,3093796,3094083,3094429,3094723,3095031, 3090905,3091232,3091487,3091789,3092124,3092587,3092828,3093451,3093874,3094227,3094477,3094797,3095290, 0 MSH5 incmpl cmpl 1,0,1,0,0,1,2,0,0,0,0,0,2,
104 NM_001159995 chr8 + 32595825 32765040 32595825 32764402 11 32595825,32605561,32614513,32727948,32742674,32749560,32754371,32756402,32759305,32760199,32763747, 32596005,32605683,32614564,32728078,32742733,32749584,32754474,32756529,32759436,32760406,32765040, 0 NRG1 incmpl cmpl 2,2,1,1,2,1,1,2,0,2,2,
73 NM_001082578 chr22_KI270876v1_alt - 59733 259897 65202 259897 13 59733,66920,67470,77102,80885,82199,82412,86420,89254,99022,102597,130777,259844, 65247,66993,67559,77142,81030,82292,82466,86481,89347,99076,102744,131002,259897, 0 RBFOX2 cmpl incmpl 0,2,0,2,1,1,1,0,0,0,0,0,1,
73 NM_001083539 chr19_KI270917v1_alt + 95406 146042 95443 126763 11 95406,96480,97260,98658,100510,103973,126151,126718,126758,126869,146019, 95477,96516,97545,98958,100804,104024,126256,126756,126771,127419,146042, 0 KIR3DS1 cmpl cmpl 0,1,1,1,1,1,1,2,1,-1,-1,
127 NM_006400 chr12 - 57530049 57547331 57530688 57547063 14 57530049,57532014,57532212,57532571,57532732,57532983,57533237,57533952,57534291,57535055,57535483,57535748,57546027,57547027, 57530775,57532106,57532315,57532643,57532810,57533022,57533303,57534097,57534452,57535154,57535545,57535846,57546096,57547331, 0 DCTN2 cmpl cmpl 0,1,0,0,0,0,0,2,0,0,1,2,0,0,
585 NM_001102596 chr7_KI270809v1_alt + 1314 5014 1314 4620 4 1314,2444,3374,4392, 1475,2606,3464,5014, 0 DTX2 incmpl cmpl 1,0,0,0,
588 NM_182705 chr17 - 439979 445940 443163 445940 2 439979,445835, 443494,445940, 0 FAM101B cmpl incmpl 2,2,
1854 NM_016098 chr6 - 166364919 166383013 166365428 166382876 4 166364919,166365973,166366794,166382805, 166365453,166366106,166366894,166383013, 0 MPC1 cmpl cmpl 2,1,2,0,
585 NM_018406 chr3_KI270924v1_alt + 3234 49268 3234 48861 38 3234,9372,10074,10512,10746,11034,11245,11528,11757,12725,12901,13132,13591,14560,14953,16279,20316,22745,24734,25953,28380,29682,30009,30936,31452,32148,33059,33728,34196,36788,38731,41669,42811,43595,44770,44929,46972,48656, 9229,9642,10320,10602,10794,11149,11285,11691,12485,12853,13088,13490,14512,14857,15945,16436,20450,22910,24890,26084,28469,29862,30135,31056,31661,32239,33227,33830,34430,36926,38913,41829,42991,43669,44835,45153,47135,49268, 0 MUC4 incmpl cmpl 0,0,0,0,0,0,1,2,0,2,1,1,1,1,1,0,1,0,0,0,2,1,1,1,1,0,1,1,1,1,1,0,1,1,0,2,1,2,
73 NM_018406 chr3_KI270935v1_alt - 117263 181832 117672 181676 47 117263,119398,121385,121703,122869,123547,124709,127643,129620,131380,131980,132583,133351,133929,134541,135493,135766,137159,139286,140480,142556,145072,148080,148571,148769,149200,149401,149584,149783,150061,150669,150804,151601,151962,152526,152622,153563,154728,155810,156477,156866,157058,157134,157451,158211,161095,181594, 117877,119561,121609,121768,122943,123727,124869,127825,129758,131614,132082,132751,133442,134138,134661,135619,135946,137248,139417,140636,142721,145206,148237,148764,149152,149353,149536,149735,150013,150474,150756,151265,151913,152475,152574,153227,154723,155762,156429,156770,156962,157086,157368,157730,161080,161346,181832, 0 MUC4 cmpl cmpl 2,1,2,0,1,1,0,1,1,1,1,1,0,1,1,1,1,2,0,0,0,1,0,2,1,1,1,0,1,2,2,0,0,0,0,1,2,1,0,1,1,0,0,1,0,1,0,
586 NM_001083539 chr19_KI270914v1_alt - 134463 135752 135148 135752 4 134463,135148,135649,135706, 135038,135187,135696,135752, 0 KIR3DS1 incmpl incmpl -1,1,2,0,
585 NM_001083539 chr19_KI270915v1_alt - 1961 52603 21246 52566 11 1961,20581,21238,21252,21753,43985,47205,49051,50464,51493,52532, 1975,21140,21250,21291,21858,44036,47499,49351,50749,51529,52603, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,1,1,0,
73 NM_001282494 chr15_KI270851v1_alt - 248544 262186 251875 262088 20 248544,252135,252386,252566,253241,253764,255088,255412,256037,256320,256534,256573,257506,257711,257884,258133,259025,259287,260250,262040, 252051,252291,252484,252667,253333,253840,255157,255669,256125,256428,256563,256621,257616,257796,257932,258172,259106,259347,260370,262186, 0 GOLGA8N cmpl cmpl 1,1,2,0,1,0,0,1,0,0,1,0,1,0,0,0,0,0,0,0,
586 NM_014218 chr19_KI270921v1_alt + 204297 237450 204335 218299 10 204297,205333,207817,209642,213090,217404,217462,217971,218122,237311, 204369,205369,208117,209936,213141,217449,217509,218024,218672,237450, 0 KIR2DL1 cmpl cmpl 0,1,1,1,1,1,2,1,0,-1,
609 NM_032470 chr6_GL000252v2_alt - 3256194 3261048 3256388 3260140 13 3256194,3256810,3257051,3257305,3257495,3257739,3257991,3258215,3258477,3258759,3258927,3259301,3259926, 3256490,3256974,3257213,3257402,3257647,3257872,3258122,3258359,3258598,3258813,3259050,3259637,3261048, 0 TNXB cmpl cmpl 0,1,1,0,1,0,1,1,0,1,1,1,0,
585 NM_004138 chr17_GL383564v2_alt + 35437 38113 35437 38113 6 35437,35965,36384,37337,37590,37892, 35769,36048,36541,37499,37716,38113, 0 KRT33A incmpl incmpl 1,0,2,0,0,0,
585 NM_138297 chr3_KI270936v1_alt + 20425 47967 20425 47560 22 20425,22919,24364,25583,27984,29286,29613,30571,31094,31790,32481,33150,33618,35474,37407,40363,41505,42289,43464,43623,45671,47355, 20564,23084,24520,25714,28073,29466,29739,30691,31303,31881,32649,33252,33852,35612,37589,40523,41685,42363,43529,43847,45834,47967, 0 MUC4 incmpl cmpl 2,0,0,0,2,1,1,1,1,0,1,1,1,1,1,0,1,1,0,2,1,2,
585 NM_138297 chr3_KI270937v1_alt + 20425 47969 20425 47560 22 20425,22919,24364,25583,27984,29286,29613,30571,31094,31790,32481,33150,33618,35474,37407,40363,41505,42289,43464,43623,45671,47355, 20564,23084,24520,25714,28073,29466,29739,30691,31303,31881,32649,33252,33852,35612,37589,40523,41685,42363,43529,43847,45834,47969, 0 MUC4 incmpl cmpl 2,0,0,0,2,1,1,1,1,0,1,1,1,1,1,0,1,1,0,2,1,2,
585 NM_001083539 chr19_KI270930v1_alt - 1961 52420 21264 52383 11 1961,20599,21256,21270,21771,43785,47006,48852,50265,51295,52349, 1975,21158,21268,21309,21876,43836,47300,49152,50550,51331,52420, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,1,1,0,
585 NM_001083539 chr19_KI270931v1_alt - 2318 52095 21619 52058 11 2318,20954,21611,21625,22126,43477,46697,48543,49956,50985,52024, 2332,21513,21623,21664,22231,43528,46991,48843,50241,51021,52095, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,1,1,0,
73 NM_031854 chr17_JH159146v1_alt - 247186 268109 247186 268065 6 247186,247437,247569,251583,267877,268016, 247332,247464,247696,251711,268003,268109, 0 KRTAP4-12 incmpl cmpl 2,2,1,2,2,0,
617 NM_005104 chr6_GL000252v2_alt + 4221379 4225039 4221379 4224251 5 4221379,4221656,4223360,4223874,4224114, 4221536,4221919,4223665,4223997,4225039, 0 BRD2 incmpl cmpl 2,0,2,1,1,
1003 NM_001282171 chr19 + 54816463 54867095 54816500 54847795 9 54816463,54819712,54821564,54825027,54847183,54847750,54847790,54847901,54867072, 54816534,54820012,54821858,54825078,54847288,54847788,54847803,54848451,54867095, 0 KIR3DS1 cmpl cmpl 0,1,1,1,1,2,1,-1,-1,
588 NM_001282171 chr19_GL949747v2_alt + 400778 402067 400778 401382 4 400778,400834,401343,401492, 400824,400881,401382,402067, 0 KIR3DS1 incmpl incmpl 0,2,2,-1,
590 NM_001282171 chr19_GL949748v2_alt + 734721 735431 734721 734766 3 734721,734762,734872, 734760,734774,735431, 0 KIR3DS1 incmpl cmpl 2,2,-1,
591 NM_001282171 chr19_GL949749v2_alt + 813244 856315 813281 855644 9 813244,816355,830882,832539,836003,855032,855599,855639,855750, 813315,816513,831024,832833,836054,855137,855637,855652,856315, 0 KIR3DS1 cmpl cmpl 0,1,0,1,1,1,2,1,-1,
591 NM_001282171 chr19_GL949750v2_alt + 819640 830388 819640 829717 7 819640,821347,824789,829105,829672,829712,829823, 819795,821622,824840,829210,829710,829725,830388, 0 KIR3DS1 incmpl cmpl 2,1,1,1,2,1,-1,
590 NM_001282171 chr19_GL949752v1_alt + 720829 771470 720866 752186 9 720829,724081,725933,729396,751574,752141,752182,752292,771447, 720900,724381,726227,729447,751679,752180,752194,752842,771470, 0 KIR3DS1 cmpl cmpl 0,1,1,1,1,2,2,-1,-1,
588 NM_001282171 chr19_GL949753v2_alt + 450525 478764 450562 478093 9 450525,453637,468042,469702,473164,477481,478048,478088,478199, 450596,453795,468184,469996,473215,477586,478086,478101,478764, 0 KIR3DS1 cmpl cmpl 0,1,0,1,1,1,2,1,-1,
585 NM_001282171 chr19_KI270883v1_alt - 1695 52345 21013 52308 9 1695,20348,21005,21019,21520,43730,46950,48796,52274, 1709,20907,21017,21058,21625,43781,47244,49096,52345, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,0,
585 NM_001282171 chr19_KI270884v1_alt - 2144 52549 21409 52512 9 2144,20744,21401,21415,21916,43931,47151,48997,52478, 2158,21303,21413,21454,22021,43982,47445,49297,52549, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,0,
585 NM_001282171 chr19_KI270885v1_alt - 2270 52912 21555 52875 9 2270,20890,21547,21561,22062,44294,47514,49360,52841, 2284,21449,21559,21600,22167,44345,47808,49660,52912, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,0,
585 NM_001282171 chr19_KI270886v1_alt - 10365 41740 11036 41703 8 10365,11028,11042,11543,33122,36342,38188,41669, 10930,11040,11081,11648,33173,36636,38488,41740, 0 KIR3DS1 cmpl cmpl -1,2,1,1,1,1,1,0,
585 NM_001282171 chr19_KI270888v1_alt - 1834 51041 21120 51004 9 1834,20455,21112,21126,21627,42423,45643,47489,50970, 1848,21014,21124,21165,21732,42474,45937,47789,51041, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,0,
585 NM_001282171 chr19_KI270889v1_alt - 1961 52603 21246 52566 9 1961,20581,21238,21252,21753,43985,47205,49051,52532, 1975,21140,21250,21291,21858,44036,47499,49351,52603, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,0,
585 NM_001282171 chr19_KI270891v1_alt - 1961 52618 21260 52581 9 1961,20595,21252,21266,21767,44000,47220,49066,52547, 1975,21154,21264,21305,21872,44051,47514,49366,52618, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,0,
18 NM_001128929 chr3 + 77098011 77649963 77098011 77646055 25 77098011,77477413,77481098,77493243,77522774,77546337,77550817,77557943,77562650,77563166,77564953,77568312,77574498,77577489,77579946,77588750,77595141,77596622,77602209,77607797,77617512,77622226,77634869,77644703,77646053, 77098340,77477571,77481219,77493382,77522902,77546462,77550989,77558149,77562732,77563329,77565120,77568434,77574730,77577614,77580118,77588933,77595184,77596750,77602491,77607954,77617773,77622432,77635043,77644904,77649963, 0 ROBO2 incmpl cmpl 2,1,0,1,2,1,0,1,0,1,2,1,0,1,0,1,1,2,1,1,2,2,1,1,1,
610 NM_004197 chr6_GL000256v2_alt + 3314929 3315373 3314929 3314976 1 3314929, 3315373, 0 STK19 incmpl cmpl 1,
585 NM_138297 chr3_KI270895v1_alt + 20425 47969 20425 47560 22 20425,22919,24364,25583,27984,29286,29613,30571,31094,31790,32481,33150,33618,35474,37407,40363,41505,42289,43464,43623,45671,47355, 20564,23084,24520,25714,28073,29466,29739,30691,31303,31881,32649,33252,33852,35612,37589,40523,41685,42363,43529,43847,45834,47969, 0 MUC4 incmpl cmpl 2,0,0,0,2,1,1,1,1,0,1,1,1,1,1,0,1,1,0,2,1,2,
585 NM_138297 chr3_KI270924v1_alt + 20311 49268 20311 48861 22 20311,22745,24734,25953,28380,29682,30009,30936,31452,32148,33059,33728,34196,36788,38731,41669,42811,43595,44770,44929,46972,48656, 20450,22910,24890,26084,28469,29862,30135,31056,31661,32239,33227,33830,34430,36926,38913,41829,42991,43669,44835,45153,47135,49268, 0 MUC4 incmpl cmpl 2,0,0,0,2,1,1,1,1,0,1,1,1,1,1,0,1,1,0,2,1,2,
585 NM_138297 chr3_KI270934v1_alt + 20425 47967 20425 47560 22 20425,22919,24364,25583,27984,29286,29613,30571,31094,31790,32481,33150,33618,35474,37407,40363,41505,42289,43464,43623,45671,47355, 20564,23084,24520,25714,28073,29466,29739,30691,31303,31881,32649,33252,33852,35612,37589,40523,41685,42363,43529,43847,45834,47967, 0 MUC4 incmpl cmpl 2,0,0,0,2,1,1,1,1,0,1,1,1,1,1,0,1,1,0,2,1,2,
76 NM_006781 chr6_GL000250v2_alt - 3655067 3704158 3655067 3703952 18 3655067,3655705,3656177,3663182,3664629,3668031,3668506,3669209,3671567,3672189,3681981,3687357,3687882,3698516,3700178,3701033,3702151,3703939, 3655089,3655726,3656201,3663203,3664650,3668052,3668527,3669230,3671588,3672228,3682071,3687378,3687905,3698546,3700211,3701066,3702238,3704158, 0 C6orf10 incmpl cmpl 1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,0,
585 NM_001102595 chr7_KI270809v1_alt + 1314 5014 1314 4620 4 1314,2444,3374,4392, 1475,2606,3464,5014, 0 DTX2 incmpl cmpl 1,0,0,0,
585 NM_014218 chr19_KI270882v1_alt - 8300 41453 27451 41415 10 8300,27069,27726,28241,28301,32609,35814,37633,40381,41381, 8430,27628,27779,28288,28346,32660,36108,37933,40417,41453, 0 KIR2DL1 cmpl cmpl -1,0,1,2,1,1,1,1,1,0,
585 NM_014218 chr19_KI270887v1_alt - 13975 47128 33126 47090 10 13975,32744,33401,33916,33976,38284,41489,43308,46056,47056, 14105,33303,33454,33963,34021,38335,41783,43608,46092,47128, 0 KIR2DL1 cmpl cmpl -1,0,1,2,1,1,1,1,1,0,
585 NM_014218 chr19_KI270916v1_alt - 2087 111711 21238 111673 10 2087,20856,21513,22028,22088,26396,29601,31420,110831,111639, 2217,21415,21566,22075,22133,26447,29895,31720,110867,111711, 0 KIR2DL1 cmpl cmpl -1,0,1,2,1,1,1,1,1,0,
104 NM_001160001 chr8 + 32595825 32765040 32595825 32764402 10 32595825,32605561,32727948,32742674,32749560,32754371,32756402,32759305,32760199,32763747, 32596005,32605683,32728078,32742733,32749584,32754474,32756529,32759436,32760406,32765040, 0 NRG1 incmpl cmpl 2,2,1,2,1,1,2,0,2,2,
589 NM_022892 chr5_KI270897v1_alt - 626937 654417 628579 654417 10 626937,628087,630425,634343,637311,638359,649294,652263,652657,654332, 628066,628658,630593,636453,637369,638441,649394,652383,652709,654417, 0 NAIP cmpl incmpl -1,2,1,1,0,2,1,1,0,2,
587 NM_006322 chr13_KI270838v1_alt - 285974 305687 286962 305687 5 285974,290550,300014,305001,305595, 287121,290667,300155,305133,305687, 0 TUBGCP3 cmpl incmpl 0,0,0,0,1,
585 NM_001102594 chr7_KI270809v1_alt + 1314 5014 1314 4620 4 1314,2444,3374,4392, 1475,2606,3464,5014, 0 DTX2 incmpl cmpl 1,0,0,0,
73 NM_001083539 chr19_KI270920v1_alt + 103335 153119 103372 133813 11 103335,104409,105189,106587,108439,111902,133201,133768,133808,133919,153016, 103406,104445,105474,106887,108733,111953,133306,133806,133821,134389,153119, 0 KIR3DS1 cmpl cmpl 0,1,1,1,1,1,1,2,1,-1,-1,
585 NM_001282170 chr19_KI270914v1_alt - 10504 42507 11175 42470 9 10504,11167,11181,11682,33892,37112,38958,41401,42436, 11069,11179,11220,11787,33943,37406,39258,41437,42507, 0 KIR3DS1 cmpl cmpl -1,2,1,1,1,1,1,1,0,
585 NM_001282170 chr19_KI270915v1_alt - 1961 52603 21246 52566 10 1961,20581,21238,21252,21753,43985,47205,49051,51493,52532, 1975,21140,21250,21291,21858,44036,47499,49351,51529,52603, 0 KIR3DS1 cmpl cmpl -1,-1,2,1,1,1,1,1,1,0,
586 NM_001256653 chr19_GL383575v2_alt - 166138 170222 168796 170222 1 166138, 170222, 0 ZNF43 cmpl incmpl 2,
1015 NM_001013356 chr11 + 56375623 56376499 56375623 56376499 2 56375623,56376431, 56376421,56376499, 0 OR8U8 cmpl incmpl 0,1,
586 NM_178826 chr12_GL383553v2_alt - 135831 152874 137402 152874 5 135831,137398,143847,147674,152762, 136612,137594,143953,147794,152874, 0 ANO4 cmpl incmpl -1,0,2,2,1,
585 NM_004522 chr2_GL582966v2_alt + 3213 96131 3213 83688 23 3213,7540,7865,8603,12829,15768,16243,33986,45347,50933,53366,55631,63021,66432,69275,70411,72434,72733,77404,79974,82146,83581,95089, 3320,7589,7921,8691,12954,15873,16392,34135,45523,51002,53573,55778,63210,66550,69352,70521,72536,72794,77476,80079,82363,83695,96131, 0 KIF5C incmpl cmpl 1,0,1,0,1,0,0,2,1,0,0,0,0,0,1,0,2,2,0,0,0,1,-1,
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genome | 22 Dec 18:16 2014

Digest for genome <at> soe.ucsc.edu - 2 updates in 2 topics

Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Dec 22 08:59AM -0800

Hello Sander,
 
Thanks for your question. The tRNA Genes track has not yet been released to
our public site. We do have it available on our preview server:
http://genome-preview.ucsc.edu/. Please note: Genome-preview allows users
to preview tracks/data before they have been through our quality assurance
process. Because genome-preview contains pre-release data, please use
discretion when downloading and viewing data from genome-preview as it may
still be undergoing changes and improvements.
 
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
On Wed, Dec 17, 2014 at 7:05 AM, Sander Claus <sander.claus <at> biogazelle.com>
wrote:
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Dec 22 08:48AM -0800

Hello Gert,
 
Thank you for your question. Our RefSeq tables are updated nightly. Please
see this previously answered question for more details:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/ClmwZbanI_g/m4tTqvuKxHoJ
 
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
On Wed, Dec 10, 2014 at 2:19 AM, Gert Hulselmans <hulselmansgert <at> gmail.com>
wrote:
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genome | 15 Dec 18:11 2014

Digest for genome <at> soe.ucsc.edu - 1 update in 1 topic

Nadine Mwemena <nadmub03 <at> hotmail.com>: Dec 14 09:56AM -0500

Hello,My name is Nadine and I am a grad student at UMUC. I need some help completing an assignment for my introduction to bioinformatics class . I tried doing it myself but I couldn't find my way around in the website. Please help. Here are the questions:
a. Using human genome Feb 2009 (Hg19), locate the gene.
Clear all tracks and only display 1. Base Position (full), 2.
RefSeq
Genes (full), 3. ENCODE Regulation (show). Take a screenshot of the gene with
those three tracks, including regions 1000 bp immediately upstream and 1000 bp downstream
of the gene.
 
b. How many mRNA transcript does this gene have? How many
exons in each transcript?
 
c. using 5 sentences or less, discuss what information does the ENCODE track provide?
I look forward to your response.
Thanks,Nadine
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genome | 5 Dec 18:06 2014

Digest for genome <at> soe.ucsc.edu - 9 updates in 7 topics

Jonathan Casper <jcasper <at> soe.ucsc.edu>: Dec 04 05:43PM -0800

Hello Hussain,
 
Thank you for your question about the divergence values displayed for items
in the RepeatMasker track. These values are calculated by the
RepeatMasker software,
and your best source of information on this topic is most likely to contact
the authors directly. That said, the information in http://www.repeatmasker
.org/webrepeatmaskerhelp.html suggests that the divergence value is simply
the percentage of bases in the matching region that were substitutions with
respect to the consensus repeat sequence.
 
I hope this is helpful. If you have any further questions, please reply to
genome <at> soe.ucsc.edu or genome-mirror <at> 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-www <at> soe.ucsc.edu.
 
--
Jonathan Casper
UCSC Genome Bioinformatics Group
 
On Fri, Nov 28, 2014 at 11:33 AM, Askree, Hussain <hussain.askree <at> emory.edu>
wrote:
 
Matthew Speir <mspeir <at> soe.ucsc.edu>: Dec 04 04:15PM -0800

Hi Brijesh,
 
Thank you for your question about getting SNP data for the IL10 gene.
There are many different variation tracks available for the hg19
assembly of the human genome,
http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19. These variation tracks
are separated into two track groups in the UCSC Genome Browser, the
"Phenotype and Literature" group and the "Variation" group. SNP tracks
under "Phenotype and Literature", such as OMIM AV SNPs or ClinVar
Variants, contain variants that have been associated with a disease
phenotype. Most of the SNP tracks under "Variation", such as All
SNPs(141) or EVS Variants, contain SNPs and other variants from various
SNP data repositories. If you are interested in any and all SNPs that
may occur in the IL10 gene, then you will mostly likely be interested in
the All SNPs(141) track,
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=snp141, which
contains SNPs from the dbSNP 141 release.
 
You can get the SNPs from the All SNPs(141) track that occur in both the
exons and introns of the IL10 gene using the Table Browser. To get this
information, use the following steps:
 
1. Navigate to the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables.
 
2. Select your assembly and tracks
 
clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Variation
track: All SNPs(141)
table: snp141
region: click the button next to position, and the enter the
position: chr1:206,940,948-206,945,839
output: all fields from selected table
output file: enter a file name to save your results to a file, or
leave blank to display results in your browser
 
3. Click "get output".
 
You can see an explanation of what the various columns in your output
represent by clicking the "describe table schema" button on the Table
Browser after you've selected the snp141 table. You can also replace the
track and table with your variation track of interest if the All
SNPs(141) track does not fit your need.
 
I hope this is helpful. If you have any further questions, please reply
to genome <at> 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-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 12/4/14, 5:13 AM, Brijesh Dabhi wrote:
Scott Wilson <livvy01 <at> uab.edu>: Dec 04 07:50PM

Dear UCSC,
 
Do your mouse genome maps include BAC contains? I am trying to find a BAC that has the MLK3 gene. Thanks.
 
Scott
Matthew Speir <mspeir <at> soe.ucsc.edu>: Dec 04 03:57PM -0800

Hi Scott,
 
Thank you for your question about getting BAC information for the MLK3
gene. We do have BAC End Pair information on the Genome Browser for the
mm9 assembly, http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm9. From that
Gateway page, you can search for your MLK3 gene to find it's position
within the genome. Please note that in our UCSC Genes track, MLK3 is
labelled as Map3k11. Click the only result under the "UCSC Genes"
section to navigate to the Genome Browser position for that gene. Then,
you will need to turn on the BAC End Pairs track. To do so, find the Bac
End Pairs track under the "Mapping and Sequencing" group, select "pack"
or "full" from the drop-down below the track name and then click
refresh. You should now see a gene track containing the MLK3 gene and
another track showing the BAC End Pairs.
 
I hope this is helpful. If you have any further questions, please reply
to genome <at> 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-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 12/4/14, 11:50 AM, Scott Wilson wrote:
Clara BENOIT <clara.benoitp <at> gmail.com>: Dec 04 07:51PM +0100

Hi,
 
I'm trying to visualize 2 bigwig files on UCSC.
I followed the step-by-step description of how to set up a track hub and I
loaded it in UCSC (with no error message). The tracks appear in the browser
but there is not any data inside... (see screenshot attached)
Here's my hub link :
https://fasterdb.lyon.unicancer.fr/UCSC_hubs/sipp_hub/hub.txt.
 
I know that my bigwig files are correct because I can visualize them in IGV
(see screenshot attached).
 
When I used hubcheck with the link above, I got this error :
*Couldn't open /Users/clarabenoit/.hg.conf , No such file or directory*
I used the following workaround : HGDB_CONF=/dev/null hubCheck
https://fasterdb.lyon.unicancer.fr/UCSC_hubs/sipp_hub/hub.txt.
And I didn't get any error message.
 
Is there a problem with my hub that is not reported by hubcheck?
 
Thanks in advance,
Clara Benoit
Brian Lee <brianlee <at> soe.ucsc.edu>: Dec 04 12:30PM -0800

Dear Clara Benoit,
 
Thank you for using the UCSC Genome Browser and your question about the
display of a hub bigWig file that is displaying at IGV. The issue stems
from the chromosome names in the bigWig files being displayed. The files
have 1 for chromosome 1 and MT for mitochondria, which are acceptable
notations at IGV, whereas the UCSC browser needs the abbreviation "chr" in
front, and uses M instead of MT.
 
Thank you for your input about hubCheck, we are planning to improve it and
will definitely include reporting this kind of error. If you have more
suggestions we would greatly enjoy hearing them!
 
Here are some steps I checked that you could use to change your annotation
files so they will display at UCSC in a hub. If you do not have the
original wiggle/bedGraph files, you will need to expand your bigWigs with
the utility "bigWigToWig", then you would perform some command line changes
to add"chr" to the front of each line and swap MT with M (and remove any
comment lines). Lastly you would repackage the wig/bedGraph back up into a
new binary bigWig with "wigToBigWig".
 
Here is the directory you would use to find the correct utility for your
operating system by running "uname -a" on the command line, then download
"bigWigToWig" and "wigToBigWig": http://hgdownload.soe.ucsc.edu/admin/exe/
 
To run the wigToBigWig function you will also need a file that outlines the
sizes of each chromosome (chrom.sizes), you can acquire it by running this
command:
curl -O http://genome.ucsc.edu/goldenPath/help/hg19.chrom.sizes
 
1. Expand your bigWig (if you don't have it already in the non-bigWig
state).
bigWigToWig accepted_hits.bw new.wig
 
2. Change the MT to a M and remove comments and add chr to the start of
every line:
cat new.wig | grep -v "#" | sed -e "s/MT/M/" | sed -e "s/^/chr/" >
new.fixed.wig
 
3. Turn the fixed.wig, that now has chrM instead of MT and chr20 instead of
20, into a bigWig
wigToBigWig new.fixed.wig hg19.chrom.sizes new.fixed.bw
 
Now you can put the URL to that new.fixed.bw into your trackDb.txt, or even
load it directly via custom tracks:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgt.customText=http://university.edu/lab/directory/new.fixed.bw
 
Thank you again for using the UCSC Genome Browser hubs feature and sharing
the issues you are having. Please feel free to reply with more feedback or
send further suggestions to our suggestion box at
http://genome.ucsc.edu/cgi-bin/hgUserSuggestion.
 
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genome Bioinformatics Group
 
On Thu, Dec 4, 2014 at 10:51 AM, Clara BENOIT <clara.benoitp <at> gmail.com>
wrote:
 
Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Dec 04 10:49AM -0800

Hello Martin,
 
Thank you for your question. From the Gateway page (
http://genome.ucsc.edu/cgi-bin/hgGateway), choose your assembly and click
the 'track search' button. Type in a search term and click 'search'. For a
description of the track, click on the track name. To turn a track on,
click the checkbox next to the track and then click 'view in browser'. For
more information about using Track Search, please refer to this help page:
http://genome.ucsc.edu/goldenPath/help/trackSearch.html.
 
If you are unfamiliar with the Genome Browser, we have a number of
resources and tutorials to help get you started:
http://genome.ucsc.edu/training.html
 
To answer your question about the Gene Sorter, yes, your results will show
matches in all chromosomes. Please see this help page for more information
on how to use and understand the Gene Sorter display:
http://genome.ucsc.edu/goldenPath/help/hgNearHelp.html.
 
If you have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
 
 
On Wed, Dec 3, 2014 at 3:13 AM, Martin Garbe <
Brian Lee <brianlee <at> soe.ucsc.edu>: Dec 04 10:11AM -0800

Dear Eric,
 
Thank you for using the UCSC Genome Browser and your question about the
last two columns in the Txn Fac ChIP tables referring to experiment IDs and
experiment scores.
 
When viewing the Table Schemas in the Table Browser, if you scroll down you
should see a Track Description page, such as the below:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV2
 
Reviewing these Track Descriptions will often help provide more details
than the one line in the schema details including these sentences: "The
first list field (expNums) contains numeric identifiers for experiments,
keyed to the wgEncodeRegTfbsClusteredInputsV3 table, which includes such
information as the experiment's underlying Uniform TFBS table name, factor
targeted, antibody used, cell type, treatment (if any), and laboratory
source. The second list field (expScores) contains the scores for the
corresponding experiments."
 
Also on theTrack Description page you will find a "downloads" link that
will bring you to a page where you can quickly acquire files, versus using
the Table Browser to output the information to a named.txt file. In this
case you could click the links for the wgEncodeRegTfbsClusteredV2.bed.gz
and wgEncodeRegTfbsClusteredV3.bed.gz files:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegTfbsClustered/
 
In essence these final two columns are metaData sharing coded information
through further associated tables to explain the experimental cell types
providing evidence for transcription factor binding at each location. If
this information is not of interest, you could ignore those last two
columns. Please see this previously answered mailing list question for
further information:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/93Rqrrs--y8/VceGRwgyh88J
 
Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply to genome <at> 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-www <at> soe.ucsc.edu.
 
All the best,
 
Brian Lee
UCSC Genome Bioinformatics Group
 
Update Watch Duplicate Copy Move
 
 
Matthew Speir <mspeir <at> soe.ucsc.edu>: Dec 04 10:10AM -0800

Hi Jie,
 
Thank you for your question about transcription factor data for Rat
(RGSC 6.0/rn6). Unfortunately, it appears that we don't provide
transcription factor data for any of the rat assemblies that we host
here at UCSC. However, you may be able to find other online resources
that contain this information.
 
I hope this is helpful. If you have any further questions, please reply
to genome <at> 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-www <at> soe.ucsc.edu.
 
Matthew Speir
UCSC Genome Bioinformatics Group
 
 
On 12/4/14, 9:03 AM, Hou, Jie (MU-Student) wrote:
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