[gmztrlmz]

Dear Sir/Madam,

First of all, I have a methylation project and I am going to study with Sparcl1 gene. I have searched CpG island of this gene in your website but I could not find anything. I want to do primer design for Realtime PCR in this gene CpG island so company want CpG island sequence for me. I tried found an island but I could not. In brief, my gene is Sparcl1(Gene ID:8404) (Chromosome position: chr4:87473330-87529503)  and I need to a CpG island sequence in this gene. Can you help me about this issue?

I am looking forward to hearing from you.

Kind Regards, 

Gamze Terlemez

MSc. Student 

Department of Biotechnology 

IZTECH

Samsung Mobile tarafından gönderildi.

[Cristina Ferreira]

Dear UCSC Genome Browser support team,

Can I directly transfer through the UCSC browser a Custom Track created by me from one session to another? 

Best regards,

 

-- 

Cristina Ferreira

Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
Campos dos Goytacazes, RJ, Brazil.

[Robert Kuhn]

Hello, Cristina,

There is a workaround for getting a custom track from one

session into another.

If Session A has a custom track, you can find the location

in our file system of the pointer to the track by going to

the cartDump page:

  http://genome.ucsc.edu/cgi-bin/cartDump

 

Somewhere on that page will be a variable that starts with

"ctfile_<assembly>."  

The value of the variable will be  "../trash/<something>."

Copy this line to a text editor of some kind.

Now load Session B (maybe in a new browser window, though

it can be the same) and go back to the cartDump page.

This page will have all the parameters for Session B

At the bottom of the page is a pair of text boxes:

"Add/alter a variable named:" and "new value."

Put the variable in the first box and value in the second 

box and Submit.

To get back to the Browser graphic, go up to the url and 

hack the url to: 

  http://genome.ucsc.edu/cgi-bin/hgTracks

  

This should take you back to the Browser graphic with all 

the same configuration of session B, but with the custom 

track loaded as well.

Save Session B again.

Thanks for using the Browser.

best regards,

   --b0b kuhn

   ucsc genome bioinformatics group

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[Robert Kuhn]

Hello, Cristina,

The Table Browser method you are using is the best way to move the data.

If you have access to a server where you can put the files, you can load them 

via url.  You could have the files on a server, then make another file with all the

urls in one file.  Loading the "wrapper" url will allow you load all the content

urls together at once.

In any case we recommend you keep a copy of your data locally as a backup

as we are not a data storage service and cannot guarantee that we will not

lose your data.

One of my colleagues suggests that you could start from Session A, with all

the custom tracks loaded, then reconfigure the data tracks to match the

conditions of the new session, then save it under the new name, Session B.

Which approach you want to take would depend on how different the sessions

are from each other.

thanks and best wishes,

       --b0b kuhn

On Mon, Feb 26, 2018 at 1:13 PM, Cristina Ferreira <ferreira...@gmail.com> wrote:

Hi, Kuhn,

Thank for your help.

Using the cartDump page, I can copy all "custom tracks" from one Session to another. A very interesting resource. Thanks for the explanation!

However, I'm interested in copying, for example, one or two specific "custom tracks" from one Session to another.

Currently I have been download the data of a "custom track" specific of a Session by "table bowser" and upload this information in a new "custom track" in another Session.

Is there a more practical way to copy the "custom track", as I mentioned?

Best regards

Cristina Ferreira

--

Cristina Ferreira

[Cristina Ferreira]

Hi, Kuhn,

Thank for your help.

Using the cartDump page, I can copy all "custom tracks" from one Session to another. A very interesting resource. Thanks for the explanation!

However, I'm interested in copying, for example, one or two specific "custom tracks" from one Session to another.

Currently I have been download the data of a "custom track" specific of a Session by "table bowser" and upload this information in a new "custom track" in another Session.

Is there a more practical way to copy the "custom track", as I mentioned?

Best regards

Cristina Ferreira

2018-02-23 21:24 GMT-03:00 Robert Kuhn <ku...@soe.ucsc.edu>:

--

Cristina Ferreira

[Cristina Ferreira]

Hello, Kunh,

Sorry to bother you again. I'm testing the use of the cartDump page and I've encountered some difficulties.

Is it possible, using this feature (cartDump), to merge the custom tracks of two sessions?

When I open session A that already has custom tracks, the variable "ctfile_ <assembly>" already exists.

In my case the variable name is "ctfile_hg19". However, in session B (with different custom tracks), the variable has the same name "ctfile_h19". This way, when I copy the variable from session A to session B, the variable from session B is completely replaced by the information I added.

I tried to modify the variable name, eg. "ctfile_chr1hg19", but I was not successful.

Is it possible to merge the custom tracks of the two sessions? That is, add the custom tracks of session A in session B without losing the custom tracks of session B.

Thanks for your help.

Cristina Ferreira

2018-02-26 18:52 GMT-03:00 Robert Kuhn <ku...@soe.ucsc.edu>:

yes, I agree it can be laborious to make a lot configuration changes.  

that's why I suggested the other method first.

good luck in your work,

        --b0b

On Mon, Feb 26, 2018 at 1:49 PM, Cristina Ferreira <ferreira...@gmail.com> wrote:

Thanks, Kuhn

Indeed I've been backing up my data. Because I was looking for another way to copy a custom track.

I also use the feature, as your colleagues have suggested, by reconfiguring the data tracks to match the conditions of the new session.

But sometimes the sessions have o lots of information and this reconfiguration is laborious, in my opinion.

Anyway, thank you again for your help.

Best regards

--

Cristina Ferreira

--

Cristina Ferreira

[Robert Kuhn]

Hello, Cristina,

I was afraid I might hear from you that you wanted to do that!

There is no way to do that.  The variable refers to a place in our

system where we store the info for all your tracks associated with

that session.  You do not have access to that.  neither do we, actually.

sorry.

>  Is it possible to merge the custom tracks of the two sessions? 

only by choosing the more complex one and adding in the tracks from the

simpler one.  But you already knew you could do that.

regards,

    --b0b

On Mon, Feb 26, 2018 at 3:34 PM, Cristina Ferreira <ferreira...@gmail.com> wrote:

Hello, Kuhn,

[Cristina Ferreira]

Ok, thanks for the clarification.

Regards,

Cristina