genome | 23 Jul 19:22 2015

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

Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Jul 23 10:07AM -0700

Hello ZengKui,
 
Thanks for your question. Unfortunately, we do not have this data available
at UCSC.
 
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, Jul 21, 2015 at 2:45 PM, Guo, ZengKui, Ph.D. <guo.zengkui <at> mayo.edu>
wrote:
 
jyoti roy <jyotiroy432 <at> gmail.com>: Jul 23 06:06PM +0530

Dear Sir/Madam,
 
Can you please provide me the list of Transposable elements with their
locations and coordinates for hg19.
 
 
Thank you
 
--
Jyoti Roy
PhD Research scholar
RNAi & Functional Genomics Lab
http://vvekslab.in
Department of Life Science
National Institute of Technology Rourkela
Rourkela , 769008
Odisha
Arijita Sarkar <arisarkar88 <at> gmail.com>: Jul 23 05:08PM +0530

Hello,
I have a query regarding transposable elements. Does the hg19
repeats annotated by repeatmasker comprise all transposable elements? All
repeats are not transposable elements. So,if I want to know the genomic
coordinates of the transposable elements specifically, in human genome,
where can I get that information? Hope you will reply soon.
 
Regards
Arijita
 
*************************************************************
Arijita Sarkar
Junior Research Fellow (JRF)
Centre of Excellence in Bioinformatics (COE)
Bose Institute
**************************************************************
Jonathan Casper <jcasper <at> soe.ucsc.edu>: Jul 22 04:34PM -0700

Hello Qiong,
 
Your wiggle files for the hg19 genome assembly have coordinates that are
specific to hg19. You will need to convert those coordinates into values
appropriate for hg18 before you can load your data on that assembly. We do
not have a tool to automatically lift wiggle files to new assemblies, but
our liftOver tool will work on a related data format: bedGraph. You may be
able to convert your wiggle data into bedGraph format, and then use our
liftOver tool at http://genome.ucsc.edu/cgi-bin/hgLiftOver to do this
conversion. The following mailing list question provides links to some
tools that may assist with converting your wiggle data into a bedGraph:
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/fIFzegiIxOw/discussion
.
 
If you prefer, you can also run liftOver on your own computer instead of on
our website. This may be necessary if your wiggle data files are
particularly large. The liftOver program can be found on our download
server at http://hgdownload.soe.ucsc.edu/admin/exe/, already compiled for
several computer architectures. If a compiled version for your computer is
not available, you may also be able to compile the program yourself from
the userApps.src.tgz source code package.
 
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
 
Samuel Fernandes <sgfernan <at> lakeheadu.ca>: Jul 22 08:07PM -0300

On the results of my search on Segmental duplication (Duplications of >1000
Bases of Non-RepeatMasked Sequence); I noticed that there are some
"orientation" on the LCRs. Some of them seems to go to the right and some
to the left.
And I could not find how to retrieve this information.
 
 
arr[hg19] Xq28(153,429,330-153,527,982)
 
chrX:153481277 >>>>>>>>>>>>>>>>
chr1:245292435<<<<
chrX:153564285<<<<<<<<<<
 
chrX:153444157>>>>>>>>>>>>>>>>>
 
 
Since now, thank you very much,
Samuel Fernandes
Jonathan Casper <jcasper <at> soe.ucsc.edu>: Jul 22 04:09PM -0700

Hello Hongen,
 
Thank you for your question about the probes listed in the affyCytoscan
table of the SNP/CNV arrays track on hg19, and I'm sorry it took so long
for us to respond! The track you are asking about was created several years
ago, and some of the information about that process was difficult to
locate. We did not filter or exclude any CytoScanHD array probes from the
list provided by Affymetrix. Instead, the reason you cannot find your
probes in our table is that they were not part of the original list. The
file that we used for this track can be found at
http://www.affymetrix.com/Auth/analysis/downloads/na32/genotyping/CytoScanHD_Array.na32.3.bed.zip
(account
required), or by following the link on Affymetrix's CytoScan HD product
page at
http://www.affymetrix.com/catalog/prod520004/AFFY/CytoScan+HD+Array+Kit+and+Reagent+Kit+Bundle#1_3
.
 
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
 
Jean Shin <jshinb <at> gmail.com>: Jul 22 03:14PM -0400

Hi,
 
I would like to use an image generated by the Genome Browser in our paper
and was wondering if there is any way to save the image with a higher
resolution.
 
(What I have been doing is: I first right-click the page, view image and
save the image - is there another way to save a higher quality image?)
 
Thank you very much!
 
Jean
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genome | 15 Jul 19:09 2015

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

Roy Blum <blum <at> molbio.mgh.harvard.edu>: Jul 15 01:12AM -0400

Dear UCSC support team,
 
Using the table download utility we have downloaded from UCSC the attached file (I hope you can open it).
This is basically the file for 5'UTR of mm9.
 
We followed this in order to obtain this table:
 
 
http://genome.ucsc.edu/cgi-bin/hgTables
clade:mammal genome:mouse assembly: July2007 mm9
Group: Genes and Gene Predictions Track: UCSC Genes
filter: mm9 kgXref Link together a Known Gene ID and a gene alias
Output format: custom track
Output file: mm9_UCSCGene_5UTR.bed
click Get Output
choose radio button of 5' UTR Exons
click Get custom track in file
 
 
However, this file holds only the gene isoforms and does not hold and gene name (gene symbol).
Could you please advise what would be the right way to obtain through UCSC the gene name that each of these isoforms belong to?
 
These are the first 5 rows from the file we downloaded:
 
 
chr1 3195984 3197398 uc007aet.1_utr5_0_0_chr1_3195985_r 0 -
chr1 3203519 3205713 uc007aet.1_utr5_1_0_chr1_3203520_r 0 -
chr1 3661429 3661579 uc007aeu.1_utr5_2_0_chr1_3661430_r 0 -
chr1 3638391 3640590 uc007aev.1_utr5_0_0_chr1_3638392_r 0 -
chr1 3648927 3648985 uc007aev.1_utr5_1_0_chr1_3648928_r 0 -
 
 
 
Thanks a lot in advance !
 
Roy Blum
 
--
Roy Blum, Ph.D.
Bioinformatics Specialist
Department of Molecular Biology
Howard Hughes Medical Institute / Mass General Hospital / Harvard Medical School
Simches Research Center 6F Room 6.624
185 Cambridge St.
Boston, MA, 02114
Mob: +1(646)-716-2875
http://blumroy.googlepages.com
Minou Bina <bina <at> purdue.edu>: Jul 14 04:31PM -0400

Hello
 
I have a small .bed file that includes specific landmarks in hg18.
How can I convert this file to a bed file corresponding to hg19?
 
Thank you
 
Minou Bina
Purdue University
Min Zhang <mzhang <at> neogenomics.com>: Jul 14 02:24PM -0400

Dear Tech support,
Can you show me how to:
 
1. Find SNP in UCSC genome browser map view and show the region (exon) and location (number)
 
2. Coordinate SNP found in HapMap with UCSC database? They have different ID. I use the SNP found in HapMap and input the region number to Illumina DesignStudio (UCSC database), but it gives me the different genes.
 
Thank you very much.
 
Min Zhang M.D.
Project Scientist III
NeoGenomics Laboratories
5 Jenner, Ste 100
Irvine, CA 92618
Phone: +1 949 206 1695 Ext 2622
mobile: +1 949 246 1110
Email: mzhang <at> neogenomics.com<mailto:mzhang <at> neogenomics.com>
[cid:image001.jpg <at> 01D0BE27.B65B1990]
 
 
________________________________
This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secured or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version.
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Sandeep Singhal <sksinghal8 <at> gmail.com>: Jul 14 10:53AM -0600

Hello,
 
I am trying to convert all my SNP data from different platform (mainly Affy
and Illumina) to one built (i.e. Built 37 or Built 38). For SNP array BED
file format is different that we received from Plink as compare to what has
been provided on UCSC website (
http://genome.ucsc.edu/FAQ/FAQformat.html#format1). Please let me know what
would be the best way to perform this analysis using liftOver.
 
Thanks
Sandeep
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genome | 4 Jul 19:26 2015

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

Huiyan <huiyanjin <at> gmail.com>: Jul 03 12:20PM -0500

chrIV 1531933
chrXV 1091291
chrVII 1090940
chrXII 1078177
chrXVI 948066
chrXIII 924431
chrII 813184
chrXIV 784333
chrX 745751
chrXI 666816
chrV 576874
chrVIII 562643
chrIX 439888
chrIII 316620
chrVI 270161
chrI 230218
chrM 85779
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genome | 20 Jun 19:40 2015

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

Jonathan Casper <jcasper <at> soe.ucsc.edu>: Jun 19 05:41PM -0700

Hello Minou,
 
Thank you for your question about displaying motifs in different colors in
a browser track. When you say that you have motifs, do you mean that you
have a set of chromosome positions that correspond to your motifs? If so,
you can turn those positions into a BED track with RGB color information to
display each motif in a color of your choice. The format for a BED track
with color is described at http://genome.ucsc.edu/FAQ/FAQformat.html#format1.
Note particularly the second of the three examples, which shows using the
RGB color field. If you do not have positions, and instead just have a set
of motif sequences, then you will need to align your motifs to a genome
assembly before you can display them. Unless you have long motifs (over 25
bases), BLAT will probably not be able to handle the alignments for you.
You may have more success with a short read alignment tool like Bowtie.
After you obtain the alignment results, then you should be able to
construct a BED track as described above.
 
You may also be interested in our oligoMatch tool, which specifically
searches for perfect sequences matches. More information about oligoMatch
can be found in the answer to this mailing list question:
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/LgyVIcTONpk/discussion
.
 
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
 
Emily Binversie <eebinversie <at> wisc.edu>: Jun 19 07:06PM

I am looking for a file with the reported GC content of the 1Mb genomic region surrounding each SNP marker (500kb each side) for the Illumina Canine HD BeadChip for canFam2 ?
 
 
GC values range from 0 to 100 (indicating the percentage of G or C base pairs) in each region surrounding each SNP marker.
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genome | 18 Jun 19:10 2015

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

Luvina Guruvadoo <luvina <at> soe.ucsc.edu>: Jun 18 10:10AM -0700

Hello Ben,
 
Thank you for contacting us. We have a browser available for the Northern
pike genome on our preview server:
http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=esoLuc1
 
Please be aware our preview site contains a lot of experimental and
untested data, and may undergo changes before it's released to our public
site.
 
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
 
 
Minou Bina <bina <at> purdue.edu>: Jun 17 02:44PM -0400

Hello
 
I have a list of motifs that I would like to display in different colors in the same track along chromosomes.
Would you please info about how it could be done. Thank you
 
Minou Bina
Purdue University
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genome | 6 Jun 19:10 2015

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

Sergei Manakov <manakov <at> caltech.edu>: Jun 05 02:34PM -0700

Hello,
 
Sorry if this was asked before, but what is a good way to get
per-nucleotide conservation scores for a region? We have a few thousand
regions of 10 to 20 bp, so we are looking to make this query as a batch.
 
thanks,
Sergei
 
 
 
 
 
 
--
Sergei (Siarhei Manakou) Manakov
 
California Institute of Technology
MC 147-75
 
land: +1 626 395 3593
 
mobile: + 1 858 729 4531
Matthew Speir <mspeir <at> soe.ucsc.edu>: Jun 05 02:41PM -0700

Hi Puneet,
 
Thank you for your question about uploading a custom track to the UCSC
Genome Browser. We're not really sure what's causing the error. Would
you be able to provide us with the file "results.wig" that you are
trying to upload? Could you also provide the "track" line,
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK, you used
when uploading this track? You can send these things to me directly if
you do not wish to share them with the public list.
 
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 6/5/15 4:33 AM, puneet rawat wrote:
Matthew Speir <mspeir <at> soe.ucsc.edu>: Jun 05 11:47AM -0700

Hi Jamie,
 
Thank you for your question about executing a potentially large query.
Could you provide more details on what you are trying to do? What is
your input format for these SNPs: rsIDs, positions, or pgSnp/VCF file?
Additionally, which of our tools were you planning on using for this
query, our main site at http://genome.ucsc.edu/, our public MySQL
server, or something else?
 
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 6/4/15 6:57 PM, Jamie Engert wrote:
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genome | 26 May 19:16 2015

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

David da Silva Pires <pires <at> iq.usp.br>: May 25 01:44PM

Hello.
 
Maybe some more information could be helpful:
 
* The commands "sed" and "sort" correspond to the versions that are
distributed with Kubuntu Linux 15.04.
* The commands "twoBitInfo" and "bedToBigBed" correspond to the versions
that are distributed with GBiB (Ubuntu 14.04.1 LTS), updated with the
command ~browser/updateBrowser.
 
If you need something more, just tell me.
 
Greetings.
 
--
David da Silva Pires
 
 
On Fri, May 22, 2015 at 4:35 PM David da Silva Pires <pires <at> iq.usp.br>
wrote:
 
Rabail Zehra <rabailzehra <at> gmail.com>: May 24 11:13PM -0700

Hi,
 
I am interested in finding out about pre-computed MKAR values for the human
genome (hg19) at UCSC.. Can you please guide me with that?
Natalia Rodchenko <rodchenk <at> usc.edu>: May 24 05:21PM -0700

Hello,
 
I need to download the set of Common SNPs from dbSNP build 137,
 
I have found this link:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
 
but it only contains the file:
 
*snp138Common.txt.gz*
for the build 138.
 
Please let me know how can I get the same file, but for build 137,
thank you, Natalia
 
 
--
Natalia Rodchenko, PhD student
Computational biology and bioinformatics,
University of Southern California,
Office: RRI316C
<sofmaia <at> gmail.com>: May 24 02:07PM

I used Alamut version 2.6 to get the PhyloP score for some variants, and I know PhyloP scores in the Alamut report are obtained from UCSC Genome Browser. Now I need to know how many species and which ones are taken into consideration.
 
 
I thank you in advance.
 
 
 
 
Best regards,
 
 
Sofia Maia
 
 
Sent from Windows Mail
Andrew Nkurunungi <andrenkun <at> yahoo.com>: May 23 02:07PM

Hello,I am a bit new in Bioinformatics but I really need help downloading this file, snp132Common.txt. I need it to begin my project work. Every time I try to download it, it says that It could not be found on the server.Thanks a lot.
AndrewAndrew NkurunungiGraduate Research AssistantBioinformatics/Computer Science.Alabama Agricultural and Mechanical University
(256) 479 2957
ankurunu <at> bulldogs.aamu.edu
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genome | 22 May 19:12 2015

Digest for genome <at> soe.ucsc.edu - 5 updates in 4 topics

"Nuket, Bilgen" <bnuket <at> rvc.ac.uk>: May 21 08:42PM

Hi,
I have two problems…
1- In my data set I used bosTau7 build as my reference genome file. Now I need to lift over variant files to UMD3.1.
To achieve that I planned have to lift over from 7 to 4 and 4 to UMD3.1.
 
Are you planning to make a chain file for bosTau7To UMD3.1 ?
2- how many bosTau7 genomes out there? I downloaded from http://support.illumina.com/sequencing/sequencing_software/igenome.html and I also use IGV whihc has bostau7 genome downloaded. But In the trying process of lifting over I realised that those file are not same. Should not they be the same?
I am very confused
 
Thank you
 
 
Bad input: the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference
 
[RVC Logo - link to RVC Website]<http://www.rvc.ac.uk> [Twitter icon - link to RVC (Official) Twitter] <http://twitter.com/RoyalVetCollege> [Facebook icon - link to RVC (Official) Facebook] <http://www.facebook.com/theRVC> [YouTube icon - link to RVC YouTube] <http://www.youtube.com/user/RoyalVetsLondon?feature=mhee> [Pinterest icon - link to RVC Pinterest] <http://pinterest.com/royalvetcollege/> [Instagram icon - link to RVC Instagram] <http://instagram.com/royalvetcollege>
 
This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.
"Steve Heitner" <steve <at> soe.ucsc.edu>: May 22 09:55AM -0700

Hello, Bilgen.
 
The liftOver files you refer to already exist:
 
bosTau7 to bosTau4/6: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau7/liftOver/
bosTau4 to bosTau6: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/liftOver/
 
The UCSC bosTau7 assembly is based on the Baylor Btau_4.6.1 assembly. There is only one Baylor Btau_4.6.1 assembly, but as with any assembly, several institutions have made it available on their sites and each institution has their own method of processing the raw data. The Illumina web site you referred to has download files from Ensembl, NCBI and UCSC. If you are intending to use the UCSC liftOver tool, I would recommend using the UCSC data wherever possible, but your query and target data should certainly be from the same institution. One of the main differences between the UCSC data and the Ensembl/NCBI data is that UCSC chromosome names include “chr” (e.g., “chr1” versus just “1” for chromosome 1). The UCSC liftOver utility requires chromosome names to include the “chr”, so it is best to just use the UCSC data files.
 
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: Nuket, Bilgen [mailto:bnuket <at> rvc.ac.uk]
Sent: Thursday, May 21, 2015 1:42 PM
To: genome <at> soe.ucsc.edu
Subject: [genome] chain file request for bosTau7To UMD3.1
 

 
Hi,
 
I have two problems…
 
1- In my data set I used bosTau7 build as my reference genome file. Now I need to lift over variant files to UMD3.1.
 
To achieve that I planned have to lift over from 7 to 4 and 4 to UMD3.1.
 

 
Are you planning to make a chain file for bosTau7To UMD3.1 ?
 
2- how many bosTau7 genomes out there? I downloaded from http://support.illumina.com/sequencing/sequencing_software/igenome.html and I also use IGV whihc has bostau7 genome downloaded. But In the trying process of lifting over I realised that those file are not same. Should not they be the same?
 
I am very confused
 

 
Thank you
 

 
Bad input: the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference
 
<http://www.rvc.ac.uk> RVC Logo - link to RVC Website <http://twitter.com/RoyalVetCollege> Twitter icon - link to RVC (Official) Twitter <http://www.facebook.com/theRVC> Facebook icon - link to RVC (Official) Facebook <http://www.youtube.com/user/RoyalVetsLondon?feature=mhee> YouTube icon - link to RVC YouTube <http://pinterest.com/royalvetcollege/> Pinterest icon - link to RVC Pinterest <http://instagram.com/royalvetcollege> Instagram icon - link to RVC Instagram
 
This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.
 
--
Yuan Jian <jayuan2008 <at> yahoo.com>: May 22 06:39AM

hello,I have downloaded blat standalone version. i can blat 20bp sequence at UCSC genome web browser, but in standalone version, i get no answer. how can i query a sequence of size 20 bp in standalone version?
thanksYu
Baochun Zhang <Baochun_Zhang <at> dfci.harvard.edu>: May 21 02:23PM -0400

Hi,
 
I am searching for the distribution of various isoforms of mouse Rapgef4 gene in different tissues/cell types, so far I can see such data available for B cells and T cells (linked through Immgen.org). Are there also data for liver and brain tissues? It seems the transcript in B and T cells lacks exon 1-4, I wonder if the full-length transcript is expressed in other tissues/cell types, such as liver and brain which are known to express high levels of total Rapgef4.
 
Thanks in advance for your help,
 
Baochun Zhang, MD, PhD
Assistant Professor, Harvard Medical School
Division of Hematologic Neoplasia
Department of Medical Oncology
Department of Cancer Immunology and AIDS
Dana-Farber Cancer Institute
450 Brookline Ave, Mayer 521B
Boston, MA 02215
 
 
 
 
 
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"Steve Heitner" <steve <at> soe.ucsc.edu>: May 21 11:09AM -0700

Hello, Vinay.
 
I assume you are following the instructions at http://genomewiki.ucsc.edu/index.php/Same_species_lift_over_construction. I have a few questions for you regarding this:
 
1. Do you have the additional kent source programs required by these scripts? (twoBitInfo, twoBitToFa, partitionSequence.pl, gensub2, blat, calc, axtChain)
 
2. Do you also have the companion script BlatJob.csh?
 
3. How did you obtain your query.2bit and target.2bit files?
 
4. Are there any error messages that might provide us additional help in diagnosing the problem?
 
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: Vinay R S [mailto:vinay.rs <at> leucinerichbio.com]
Sent: Thursday, May 21, 2015 3:10 AM
To: genome <at> soe.ucsc.edu
Subject: [genome] Plasmodium falciparum liftover
 

 
Hi all,
 
I tried running available scripts for liftover(SameSpeciesBlatSetup.sh and SameSpeciesChainNet.sh) for Plasmodium falciparum 2008 to 2015,
I am not getting the .psl output or chain out puts.
Till chromosome sequence size is printing along with joblist but i am not getting any out put.
Could someone help me with this
Thanks in advance.
 
Regards
Vinay R S
 
--
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genome | 21 May 19:07 2015

Digest for genome <at> soe.ucsc.edu - 7 updates in 5 topics

Vinay R S <vinay.rs <at> leucinerichbio.com>: May 21 03:40PM +0530

Hi all,
I tried running available scripts for liftover(SameSpeciesBlatSetup.sh and
SameSpeciesChainNet.sh) for Plasmodium falciparum 2008 to 2015,
I am not getting the .psl output or chain out puts.
Till chromosome sequence size is printing along with joblist but i am not
getting any out put.
Could someone help me with this
Thanks in advance.
 
Regards
Vinay R S
Jonathan Casper <jcasper <at> soe.ucsc.edu>: May 20 02:53PM -0700

Hello Amit,
 
Thank you for your question about support for HGVS nomenclature. While we
do have plans to add support for HGVS names to our tools, there is no
timetable for it right now. Some suggestions for working around this
limitation are described in this mailing list question:
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/oMVq6Z9p_0k/discussion.
Please note that the Variant Annotation Integrator (
http://genome.ucsc.edu/cgi-bin/hgVai) does now support the entry of rs# IDs
from dbSNP - under the "Select Variants" drop down menu, select the
"Variant Identifiers" option.
 
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
 
David da Silva Pires <pires <at> iq.usp.br>: May 20 05:47PM

Hi.
 
I have build a bigBed track called "SMPs v5.2" at the following assembly
hub:
 
http://www.vision.ime.usp.br/~davidsp/hub/geneNetwork2/hub.txt
 
Since this track was obtained from a bed 12 file, every feature has the
information about the number of blocks, blocks starts and blocks sizes.
But, when I click at a feature to access its specific information page,
there is no way to download just the coding sequence (CDS). The option that
is displayed is relative to the entire window, including introns and
intergenic regions.
 
What am I supposed to do in order to download just the CDS?
 
Tranks.
 
--
David da Silva Pires
Jonathan Casper <jcasper <at> soe.ucsc.edu>: May 20 01:04PM -0700

Hello David,
 
Thank you for your question about obtaining CDS sequence for items in your
BED 12 track. We would like to improve the DNA retrieval options for the
description pages of individual features, but there is no timetable for it
right now. In the interim, the easiest way to get the sequence filtering
options you describe is to use the Table Browser. First load your hub on
our site, and then follow these steps:
 
1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables (or
click "Table Browser" from the top "Tools" menu on our site).
2. Select your track hub and track from the drop-down menus, set the region
to "genome", then click the "Identifiers: paste list" button.
3. On the new page, add the name of the BED 12 item that you want sequence
from to the text box. Click "submit".
4. Select the output format "sequence" and click "get output".
 
On the resulting page, you should be able to choose which portions of your
feature to retrieve sequence for (CDS, exons, UTR, etc.).
 
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 Wed, May 20, 2015 at 10:47 AM, David da Silva Pires <pires <at> iq.usp.br>
wrote:
 
David da Silva Pires <pires <at> iq.usp.br>: May 20 05:55PM

Hello.
 
One of my colleagues noted that all the genes for which the search is
successful have names starting with "Chr_" (the longest ones). The searches
that fail are all from scaffolds ou mitochondrial DNA (the shortest ones).
 
Is this an undocumented feature? Should the genome and, subsequently, all
the tracks relative to this genome, have its chromosomes names starting
with "Chr_" as a prerequisite in order to the search tool work?
 
Tranks.
 
 
On Tue, May 19, 2015 at 10:05 PM David da Silva Pires <pires <at> iq.usp.br>
wrote:
 
Jonathan Casper <jcasper <at> soe.ucsc.edu>: May 20 12:38PM -0700

Hello David,
 
Thank you for your question about a problem with the search index for your
bigBed. We are able to see the issue with your bigBed file, but have been
unable to reproduce it with anything we create ourselves. Are you able to
send us the data files and the program binaries (e.g., bedToBigBed) that
you used to construct your smps.bb file? You can send them to me privately
to avoid sharing with the mailing list if you prefer.
 
One of our engineers notes that search names are not required to start with
"Chr_"; we suspect that another bug is responsible.
 
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 Wed, May 20, 2015 at 10:55 AM, David da Silva Pires <pires <at> iq.usp.br>
wrote:
 
Brian Lee <brianlee <at> soe.ucsc.edu>: May 20 12:27PM -0700

Dear Jonghun Lee,
 
Thank you for using the UCSC Genome Browser and your question about Whole
Genome Bisulfite Sequencing (WGBS) data from ENCODE.
 
This data was not released to the public UCSC Genome Browser site, due to
the complexity of perfecting alignment methods, but is available at GEO and
also at the current ENCODE Portal:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1002650
https://www.encodeproject.org/experiments/ENCSR000AJI/
 
On the ENCODE portal you will find a "General protocol" Track Description
document which states these data were produced by the Dr. Richard Myers Lab
at the HudsonAlpha Institute for Biotechnology and lists Dr. Florencia
Pauli, fpauli at hudsonalpha.org, as the contact for this data.
 
Please send any data questions about the track to the source laboratory.
 
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
 
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genome | 9 May 19:23 2015

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

Jonathan Casper <jcasper <at> soe.ucsc.edu>: May 08 04:36PM -0700

Hello Ivan,
 
Thank you for checking up on this. The mid-April update to build 142 is
something that we would like to incorporate, but at this point build 144 is
likely to be released by the time that we would have the corrected version
of 142 ready for display. The plan for now is that our next update will be
for the release of SNP 144 data. We are keeping a close eye on the progress
of 144 and may reconsider if it is significantly delayed.
 
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 Mon, May 4, 2015 at 6:43 PM, Ivan Adzhubey <
Matthew Speir <mspeir <at> soe.ucsc.edu>: May 08 11:43AM -0700

Hi Mehar,
 
Thank you for your question about converting your coordinates between
hg19 and canFam3 using liftOver. If you modify your original bed file to
include the hg19 coordinates in the name column, then these will be
carried over to the output file from liftOver. This means that if your
input file contained a line like:
 
chr21 33031596 33041570 SOD1.chr21.33031596.33041570
 
Then your output region would contain "SOD1.chr21.33031596.33041570" in
the name column, thus preserving the hg19 coordinates in the canFam3
output file. You can use a command like
 
awk '{print $1,$2,$3,$4 "." $1 "." $2 "." $3}' yourOriginal.bed >
newFileWithPositionNames.bed
 
to modify your original file to include the position in the name column.
You can then use this "newFileWithPositionNames.bed" file as your input
for liftOver. If you already have periods in the names of your regions,
you can replace the periods with anything but spaces.
 
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 5/7/15 2:58 PM, mehar wrote:
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genome | 8 May 19:10 2015

Digest for genome <at> soe.ucsc.edu - 4 updates in 3 topics

Matt Jones <jonesmr9 <at> gmail.com>: May 07 12:38PM -0600

Hello,
 
I am mapping exome data to divergent reference genome and I was wondering
if you could provide liftover files for chinese hamster (criGri1) to mouse
(mm9) and squirrel (speTri2) to mouse (mm9). Thank you!
 
Best,
Matt
 
--
Matt Jones
Ph.D Student
University of Montana
Department of Organismal Biology and Ecology
matthew2.jones <at> umontana.edu
matthewrjones.com
Matthew Speir <mspeir <at> soe.ucsc.edu>: May 08 10:03AM -0700

Hi Matt,
 
Thank you for your question about these liftOver files. Unfortunately,
we don't have plans to create these liftOver files. However, you can
still carry out these conversions using our existing liftOver files in a
stepwise fashion. To go from speTri2 to mm9, use the following steps:
1. Lift coordinates from speTri2 to mm10 using this file:
http://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToSpeTri2.over.chain.gz
2. Then lift from mm10 to mm9 using this file:
http://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToMm9.over.chain.gz
 
To convert you coordinates from criGri1 to mm9, use the following steps:
1. Lift coordinates between criGri1 and hg19 using this file:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToCriGri1.over.chain.gz
2. Then lift from hg19 to mm9 using this file:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToMm9.over.chain.gz
 
Alternatively, if you want to go directly from speTri2 or criGri1 to
mm9, you can create the liftOver files yourself. To do so, please refer
to the following GenomeWiki page:
http://genomewiki.cse.ucsc.edu/index.php/Whole_genome_alignment_howto.
 
Lastly, one of our engineers provided the following input on mapping
your exome sequences between species:
"I would recommend they take the exome sequences they have and blat
them against the target of interest."
 
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 5/7/15 11:38 AM, Matt Jones wrote:
Joy Lee <joylee555350 <at> gmail.com>: May 07 04:59PM -0700

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50
mehar <meharji.arumilli <at> helsinki.fi>: May 08 12:58AM +0300

Dear all,
 
I have downloaded the liftover executable and hg19ToCanFam3 chain file
to lift hg19 coordinates to canFam3 coordinates in the below shown way:
 
./liftOver hg19.bed hg19ToCanFam3.over.chain.gz canFam3.bed failed.bed
 
The command processed and gave canFam3.bed file with canFam3
coordinates. However, i would like to have the coordinates of both hg19
and canFam3
in the output files inorder to know corresponding coordinates in both
genome assemblies. COuld someone help if there is a way to get this. Thanks.
 
Br
Mehar
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