resolution of .ps files

[Minou Bina]

Hi

I wish to thank you for all your efforts to make the genome browser such a great resource to the scientific community.

Would it be possible for you to increase the resolution of .ps images of maps created on the browser?

Occasionally, in publications the figures of the images appear very drab.

Also, in a recently submitted manuscript, the images were very blurry, I had to contact the publisher to resolve that problem but it is not clear what could be done.

Yours truly,

Minou Bina
Purdue University



----- Original Message -----
From: gen...@soe.ucsc.edu
To: Digest recipients <gen...@soe.ucsc.edu>
Sent: Tue, 28 Oct 2014 13:23:41 -0400 (EDT)
Subject: [genome] Digest for gen...@soe.ucsc.edu - 9 updates in 8 topics

=============================================================================
Today's topic summary
=============================================================================

Group: gen...@soe.ucsc.edu
Url:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/topics


- Question about retrogene track [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/532d24f1d5f03267
- URGENT pls: UCSC [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b1f588d55d5d2949
- how to change the ENCODE track color [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/ef4ccfbf2438aef9
- Feline Genome {http://public.dobzhanskycenter.ru/Hub/hub.txt} Data [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/964f1ea30d9233f0
- is MySQL required for liftOver? [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d686457b4a7a295d
- Liftover Tool [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/8cfcf3e622817c49
- Gene Sorter for chicken genome [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/411af238fe3fcc5d
- SNP coordinates Table Browser [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/de0de05d639931d6


=============================================================================
Topic: Question about retrogene track
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/532d24f1d5f03267
=============================================================================

---------- 1 of 1 ----------
From: Katrin Rademacher <katrin.r...@uni-due.de>
Date: Oct 28 03:51PM +0100
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f189584d2a0a0811

hallo,

I have a question about the retrogene track and the labeling of
retrogenes. What is the difference between the expressed retrogenes
from the ucscRetroExpressed5 table and the retrogenes from the
ucscRetroInfo5 table, which are labelled with -2 (which stands for
expressed retrogenes as well)?

If I download the ucscRetroExpressed5 table, there are also retrogenes
inside labelled with 1 (stands for pseudogene).

Can you explain the difference to me?

Thanks in advance,

Katrin Rademacher

--
Katrin Rademacher
M.Sc. Bioinformatics and Genome Research
Institut für Humangenetik
Universitätsklinikum Essen
Hufelandstrasse 55
D-45122 Essen (Germany)
Tel: +49 (201) 723 4533
Fax: +49 (201) 723 5900
E-Mail: katrin.r...@uni-due.de



=============================================================================
Topic: URGENT pls: UCSC
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b1f588d55d5d2949
=============================================================================

---------- 1 of 1 ----------
From: Nazanin Nourbehesht <nazaninno...@gmail.com>
Date: Oct 27 05:40PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/d5996f652ba0b6bd

Hi,
Would you pls be kind and help me to solve my 2 questions on how to work
with UCSC to get the proper answers

A. How can I find the below points for *HoxA1 to A13, HoxB1 to B9, HoxC4 to
C13 and HoxD1 to D13*?

*SNP density*
*Repeat content *
*Conservation (estimate)*
*Encode regulation (estimate) *



B. I should tell : whether the original definition of cluster length
(distance from outermost edges of first to last gene) is appropriate, and
using the DNA strand context of the cluster, estimate by how many kb the
cluster should be extended or reduced.


for this part i should answer:


*Original length appropriate ? (Y/N)*

*5' adjustment*

*3' adjustment *

*justification for length change*



I really do appreciate to reply me back urgently as I should have answer by
this WED.


Best Regards

Nazanin



=============================================================================
Topic: how to change the ENCODE track color
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/ef4ccfbf2438aef9
=============================================================================

---------- 1 of 1 ----------
From: Jonathan Casper <jca...@soe.ucsc.edu>
Date: Oct 27 04:56PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/bd0b7be7b8c30cfc

Hello Ming Tang,

Thank you for your question about changing the color of ENCODE browser
tracks. Unfortunately there is no way to change the color of these tracks
using the browser; they are set in internal track files. What you can do,
however, is create a custom track or track hub using the same data files.
Then you can adjust the colors of your own tracks however you like.

Download links for the ENCODE data files are available at
http://genome.ucsc.edu/ENCODE/downloads.html. In particular, the bigWig and
bigBed data files for hg19 ENCODE tracks can be found at
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/. You do not have
to download these files yourself; instead, you can just create a custom
track or track hub that points to the URL of these files on our download
server. The basic format for a custom track line to load one of these files
is as follows:

track type=bigBed name="Color example bigBed" description="Go to
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/ to find your
indexed binary bigWig or bigBed of interest"
bigDataUrl=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqGm12891R2x75Il200JunctionsRep1V3.bigBed
color=0,0,255,

track type=bigWig name="Color example bigWig" description="Go to
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/ to find your
indexed binary bigWig or bigBed of interest"
bigDataUrl=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1.bigWig
color=255,100,255,

Building a track hub that points to these files gives you even greater
control over how they are displayed. More information on constructing a
track hub is available in the Track Hub User's Guide
<http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html> and the other
links provided at
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TrackHubs.

I hope this is helpful. If you have any further questions, please reply to
gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those
addresses will be archived in publicly-accessible forums for the benefit of
other users. If your question contains sensitive data, you may send it
instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group




=============================================================================
Topic: Feline Genome {http://public.dobzhanskycenter.ru/Hub/hub.txt} Data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/964f1ea30d9233f0
=============================================================================

---------- 1 of 1 ----------
From: "Steve Heitner" <st...@soe.ucsc.edu>
Date: Oct 27 11:46AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/819dd979eb0866d2

Hello, Rosanne.

Thank you for reporting this. You have identified a shortcoming in our code. We are working on fixing this, but the fix will not be available on our public site until our next release which is currently scheduled for Wednesday November 12. It will likely be available on our test server sooner than this, however, and I can let you know when that happens.

Please contact us again at gen...@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 genom...@soe.ucsc.edu.

---
Steve Heitner
UCSC Genome Bioinformatics Group



From: Jepson, Rosanne [mailto:rje...@RVC.AC.UK]
Sent: Friday, October 24, 2014 7:48 AM
To: gen...@soe.ucsc.edu
Subject: [genome] Feline Genome {http://public.dobzhanskycenter.ru/Hub/hub.txt} Data



Dear UCSC,I am trying to extract Boris SNV data from the recently released dobzhanskycenter hub using the ICGSC Felis_catus 6.2/felCat5 assembly. To do this I have been using the Table browser with the settings detailed below.

However, I get an error message (see below).

I have also tried chaining the output format to ‘selected fields from primary table’ and limiting the data requested but without success.

I wondered if there is something straight forwards that I am not doing in order to extract this data?



Any help gratefully received!

Best wishes

Rosanne











Rosanne E. Jepson BVSc MVetMed PhD DipACVIM DipECVIM MRCVS

Lecturer in Small Animal Internal Medicine



Department of Clinical Science and Services

Royal Veterinary College



Tel (QMHA): +44 (0) 1707 666366

Tel (Office): +44 (0) 1707 667033

Fax: +44 (0) 1707 649384

Email: <mailto:rje...@rvc.ac.uk> rje...@rvc.ac.uk








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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.

--



=============================================================================
Topic: is MySQL required for liftOver?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d686457b4a7a295d
=============================================================================

---------- 1 of 2 ----------
From: Vasily Aushev <vau...@gmail.com>
Date: Oct 26 04:40AM +0300
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/60556427cd83baf6

hello,
I tried to compile liftOver sources under Windows using minGW
(GNU-compatible compiler). Unfortunately minGW's 'make' ends with errors:
/usr/bin/sh: mysql_config: command not found
/usr/bin/sh: mysql_config: command not found
../../inc/common.mk:193: *** can not find installed mysql development
system. Stop.

I am wondering if there is any way to overcome this. (In fact I have MySQL
installed but probably it is somehow not 'visible' for compiler) Do we
really need mySQL for liftOver functionality?

Thanks in advance.


---------- 2 of 2 ----------
From: Hiram Clawson <hi...@soe.ucsc.edu>
Date: Oct 27 09:28AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/73dbcd8fd1125c20

Good Morning Vasily:

You can use the shell environment variables:
MYSQLINC and MYSQLLIBS
to override the automatic detection of where MySQL
include files and libraries are located.
For example:

export MYSQLINC=/usr/local/mysql/include/mysql
export MYSQLLIBS="/usr/local/mysql/lib/mysql/libmysqlclient.a -lz"

--Hiram

On 10/25/14 6:40 PM, Vasily Aushev wrote:



=============================================================================
Topic: Liftover Tool
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/8cfcf3e622817c49
=============================================================================

---------- 1 of 1 ----------
From: "Barb, Jennifer (NIH/CIT) [E]" <ba...@mail.nih.gov>
Date: Oct 27 04:19PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/4548975141f4358c

Hello All,
I need to convert mm9 coordinates to mm10 coordinates and I tried the Liftover tool. It seems to have worked however, I lose the mm9-mm10 connection.
Is there a way to keep an ID that will link up the mm9 to the mm10 coordinate?

For example, I upload 200,000 mm9 coordinates. I get back 199,997 mm10 coordinates but there is no way that I can see that I can know for sure which coordinate maps to or goes with which coordinate from my query.

Is there a way to do this but keeping the original coordinate in the result file or possibly keeping an identifier?

This seems like it would be a common issue.

Thank you,
Jennifer


---------------------------------------------------------------------------------
Jennifer J. Barb, PhD, Staff Scientist, Mathematical and Statistical Computing Lab, Center for Information Technology, National Institutes of Health
12 South Drive, Bldg 12A, Room 2001, Bethesda, MD 20892, Office ph: 301-435-9232



=============================================================================
Topic: Gene Sorter for chicken genome
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/411af238fe3fcc5d
=============================================================================

---------- 1 of 1 ----------
From: "Raymond .Enke" <raymon...@gmail.com>
Date: Oct 26 05:19PM -0400
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a0879eff30b4bef

Hello,

Are there any plans to expand the Gene Sorter tool out to other genomes,
particularly the chicken genome? Is There currently another tool that you
can recommend for identifying gene ontology terms from a list of Gallus
gallus gene names?

Thanks,

Ray

R. Enke Ph.D.
Assistant Professor
James Madison University
Department of Biology
office: 3016G
lab: 3022
540-568-5635



=============================================================================
Topic: SNP coordinates Table Browser
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/de0de05d639931d6
=============================================================================

---------- 1 of 1 ----------
From: "Diego Pereira" <pereira...@gmail.com>
Date: Oct 24 08:00PM -0500
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/416285d1e16db9f8

Thank you Jonathan!

The BED coordinates format for the SNPs is kind of weird though. ;)

Best,

Diego



From: Jonathan Casper [mailto:jca...@soe.ucsc.edu]
Sent: Friday, October 24, 2014 7:25 PM
To: Diego Pereira
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] SNP coordinates Table Browser



Hello Diego,

Thank you for pointing this out! This is a bug in the "define regions" section of the UCSC Table Browser that had escaped our notice. Our engineers will work on fixing this issue. In the meantime, there is a work-around. The restriction is imposed for the "define regions" part of the Table Browser, but is not imposed when you add custom BED tracks. You should be able to perform searches with the Table Browser by first building a custom track with your regions of interest, and then using the Table Browser "intersection" tool to intersect your custom track with whichever track you are looking at. More information on using the intersection tool is available at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection.

Please note, however, that using the same start and end coordinate has a special meaning when using a BED file. The BED format uses 0-based, half-open coordinates (http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms). In that system, "chr1 500 500" describes a location that both starts and ends in the same location between bases. In other words, it describes an insertion. If you would like to describe a single base substitution for your SNP, the BED coordinates should instead be "chr1 500 501", which corresponds to chr1:500-500 in that coordinate format.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> or genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> . Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> .

<https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif>

--
Jonathan Casper
UCSC Genome Bioinformatics Group



On Thu, Oct 23, 2014 at 5:11 PM, Diego Pereira <pereira...@gmail.com <mailto:pereira...@gmail.com> > wrote:

Hello Jonathan,



I’m using the main server.



The error I receive is the following:



Warning/Error(s):

* chromStart (133540131) must be less than chromEnd (chrZ:133540131)
* illegal input at line 1: chrZ 133540131 133540131



Maybe I’m missing something...



Best,



Diego





From: Jonathan Casper [mailto:jca...@soe.ucsc.edu <mailto:jca...@soe.ucsc.edu> ]
Sent: Thursday, October 23, 2014 4:05 PM
To: Diego Pereira
Cc: gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
Subject: Re: [genome] SNP coordinates Table Browser



Hello Diego,

Thank you for your question about uploading SNP coordinates. The "chrZ 100 100 mySNP" format you describe worked fine for me, either when pasted into the text box of the custom track tool or when uploaded as the text of a file. Are you using our main server at http://genome.ucsc.edu <http://genome.ucsc.edu/> or one of our mirrors? What is the exact text of the error message that you receive?

If you have any further questions, please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu> or genome...@soe.ucsc.edu <mailto:genome...@soe.ucsc.edu> . Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu> .

--
Jonathan Casper
UCSC Genome Bioinformatics Group



On Tue, Oct 21, 2014 at 4:16 PM, Diego Pereira <pereira...@gmail.com <mailto:pereira...@gmail.com> > wrote:

Dear all,



In the past I was able to upload the coordinates of my SNPs using the same position for the start and end base,

i.e. chrZ 100 100 mySNP.

Today I realized that the rule has changed, and an error is triggered if my bed file contains the aforementioned format, telling me that I the end position should be greater than the start position,

i.e. chrZ 100 101 mySNP.



May I ask you to revert that rule if you find it appropriate?



Thanks,



Diego

--






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[Jonathan Casper]

Hello Minou,

Thank you for your question about the resolution of postscript images. By "maps" do you mean images of tracks on the UCSC Genome Browser from the View >> PS/PDF menu option at http://genome.ucsc.edu/cgi-bin/hgTracks? If so, the resolution of those images is set from the configuration page. Just click the "configure" button below the track image, and you will be taken to a page where you can change the image width in pixels, the label area width, and several other properties.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

--

[Minou Bina]

Hello
Previously, I asked about the resolution of .ps files

Your answer did not pertain to what I was asking.

On the top of the browser, there is a pull down menu that includes PDF/PS

My question is whether you could increase the resolution of the PS file that is offered for download.

Resolution: higher pixels/inch in the file.

Thank you

Minou Bina
Purdue University



- resolution of .ps files [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b242b9244f3f2494
- rn6 GTF question [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6490c59bc5744997
- rat rn6 GTF chrY_KL568139v1_random question [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/15c0bfc7579be0d2
- New genome assembly genome in GBiB [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/fffe6b448f742465
- 答复: [genome] liftover files of Bos_taurus_UMD_3.1/bosTau6 [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/83196724d9a4f344
- CSHL Long RNA-seq track views [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/177ebe70c1fe761e


=============================================================================
Topic: resolution of .ps files
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b242b9244f3f2494

=============================================================================

---------- 1 of 1 ----------
From: Jonathan Casper <jca...@soe.ucsc.edu>

Date: Oct 31 10:06AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/aceb4a05e1cf30e2

Hello Minou,

Thank you for your question about the resolution of postscript images. By
"maps" do you mean images of tracks on the UCSC Genome Browser from the
View >> PS/PDF menu option at http://genome.ucsc.edu/cgi-bin/hgTracks? If
so, the resolution of those images is set from the configuration page. Just
click the "configure" button below the track image, and you will be taken
to a page where you can change the image width in pixels, the label area
width, and several other properties.

I hope this is helpful. If you have any further questions, please reply to
gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those
addresses will be archived in publicly-accessible forums for the benefit of
other users. If your question contains sensitive data, you may send it
instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

=============================================================================
Topic: rn6 GTF question
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6490c59bc5744997

=============================================================================

---------- 1 of 1 ----------

From: Christa-Lynn Blenck <Christa...@Colorado.EDU>
Date: Oct 31 10:47AM -0600
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/8cb164561b7d13a2

Thanks again for your help, sorry for the delayed response to this question. Since the chrM sequence is that same between rn5 and rn6, if I simply merge the rn5 mitochondrial GTF with my rn6 GTF will that be sufficient? I am just making sure that there aren't any differences in coordinates between the two that could alter my analysis in any way.

Christa Blenck



=============================================================================
Topic: rat rn6 GTF chrY_KL568139v1_random question
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/15c0bfc7579be0d2

=============================================================================

---------- 1 of 1 ----------

From: Christa-Lynn Blenck <Christa...@Colorado.EDU>
Date: Oct 31 10:29AM -0600
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f2fe88077a0f57cf

Hello,

I have been using a GTF file from your website from the rat rn6 assembly and I noticed that there is a region titled: chrY_KL568139v1_random. I was wondering what this region consisted of? Also, I noticed that there is a gene (NM_001166307) that appears to be located on the chrY_KL568139v1_random region, as well as chr5 and chr7. A NM_001166307_dupl can also be found on chr7 as well. I was just wondering what the reason for this was as well? Is it just a region with a lot of repeats/duplicated sequences?

Thanks for the help,

Christa Blenck


Graduate student
University of Colorado at Boulder



=============================================================================
Topic: New genome assembly genome in GBiB
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/fffe6b448f742465

=============================================================================

---------- 1 of 2 ----------

From: David da Silva Pires <pi...@iq.usp.br>
Date: Oct 30 07:13PM -0200
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/500fda58884127be

Hi! Thank you very much by the release of Genome Browser in a Box. It has
saved me a lot of work!

I read all the documentation at
http://genome.ucsc.edu/goldenPath/help/gbib.html
but is not clear to me if it is possible to add a new genome assembly to
GBiB.

I would like to add the genome of Schistosoma mansoni, along with many
track hubs and custom annotation tracks. Although I saw that it is possible
to add the latter two, I can't find any information about including a new
genome. Is that possible? If it is, is the same way that would be followed
to include a new genome assembly at a UCSC Genome Browser mirror?

Besides that, I think that it is very hard to find information about how to
include a new genome assembly. Do you recommend a specific URL? Sorry if
the question is so basic, but I am a newbie at UCSC Genome Browser.

Thanks in advance.

--
David da Silva Pires

---------- 2 of 2 ----------

From: Matthew Speir <msp...@soe.ucsc.edu>
Date: Oct 31 09:42AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1a1f61ae6bda453

Hi David,

Thank you for your question about adding a new assembly to the Genome
Browser in a Box (GBiB). You can add a new assembly to your GBiB by
creating an assembly hub. Our assembly hub feature is an extension of
the track hub feature that allows you to specify your own sequence file
and related annotations. For more information on crating your own
assembly hub, please see the following help pages:

* http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
* http://genomewiki.ucsc.edu/index.php/Assembly_Hubs

If you create the assembly hub locally on your computer, you can add it
to GBiB by sharing the folder with GBiB according to the "Loading local
big data tracks and track hubs" section:
http://genome.ucsc.edu/goldenPath/help/gbib.html#LocalTracks. You can
also use GBiB to create the 2bit and big data files for your assembly
hub by following the instructions for downloading and using the Genome
Browser utilities through GBiB in the "Data and track conversion tools"
paragraph of that section.

I hope this is helpful. If you have any further questions, please reply

to gen...@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 genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group


On 10/30/14, 2:13 PM, David da Silva Pires wrote:



=============================================================================
Topic: 答复: [genome] liftover files of Bos_taurus_UMD_3.1/bosTau6
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/83196724d9a4f344

=============================================================================

---------- 1 of 1 ----------
From: Jonathan Casper <jca...@soe.ucsc.edu>

Date: Oct 30 05:37PM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/bfb82845ea72cfc6

Hello Wenjuan,

The liftOver chains for bosTau6 <-> equCab2, bosTau8 <-> equCab2, and
bosTau6 <-> canFam3 are now all available on our test download server at
http://hgdownload-test.soe.ucsc.edu. They have passed review by our QA
department, and will be available for download from our main server at
http://hgdownload.soe.ucsc.edu at the beginning of next week.

I'm sorry to say that I cannot tell you whether your reviewer will like
your results or not - that is entirely the decision of the reviewer. One of
our engineers notes that the liftOver chains we provide are already done
with
lastz and are applicable to cross species comparisons. The engineer
continues, however, to say that lifting is a different job than analyzing
ancestral relationships. You may need to run your own scientific
calculations for that purpose.

Unfortunately, we do not have the resources to continue building liftOver
chains immediately upon request. We do provide liftOver chains from the
bosTau7 cow assembly to the sheep and pig genomes:
bosTau7ToOviAri3.over.chain.gz is available on our test download server at
http://hgdownload-test.soe.ucsc.edu (please use discretion with this file,
as it has not yet been reviewed by our quality assurance team), and
bosTau7ToSusScr2.over.chain.gz is available on our main download server at
http://hgdownload.soe.ucsc.edu. If you are interested in creating other
liftOver files yourself, we provide an overview of how to build your own
liftOver chains at http://genomewiki.ucsc.edu/index.php/LiftOver_Howto.

I hope this is helpful. If you have any further questions, please reply to
gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those
addresses will be archived in publicly-accessible forums for the benefit of
other users. If your question contains sensitive data, you may send it
instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

On Tue, Oct 28, 2014 at 7:14 PM, 朱文娟(Wenjuan.zhu) <



=============================================================================
Topic: CSHL Long RNA-seq track views
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/177ebe70c1fe761e

=============================================================================

---------- 1 of 1 ----------
From: Diego Pereira <pereira...@gmail.com>

Date: Oct 30 02:52PM -0500
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/5fa8673ae0f3d692

Thank you Brian.

[Hiram Clawson]

Good Afternoon Dr. Bina:

You can set the screen size to 25,000 pixels wide and up to 32,000 pixels high.
Use the configuration page to set the width. The height depends upon what tracks
you are displaying. This resolution would be thousands of pixels per inch
in the pdf format on ordinary size paper. Even large poster prints would have
plenty of pixels per inch resolution.

--Hiram