from: JOANA DE BRITO LOURENCO SEQUEIRA MENDES <jsequeiramendes@cbm.csic.es>
to: "Norris, David" <dcnorris@uncc.edu>
cc: "Loraine, Ann" <Ann.Loraine@uncc.edu>,
"ktsuttlemyre@gmail.com" <ktsuttlemyre@gmail.com>
date: Wed, Apr 30, 2014 at 12:26 PM
subject: Re: IGB problems

Hi David, hi all,

I've done the empty cache today before doing a new session from scratch.
I'll reset the preferences to default then.

Thanks again for the curated sessions.

All the best,

Joana

"Norris, David" <dcnorris@uncc.edu> escribió:

from: Norris, David <dcnorris@uncc.edu>
to: "JOANA.DE BRITO LOURENCO.SEQUEIRA MENDES.596874" <jsequeiramendes@cbm.csic.es>,
"Loraine, Ann" <Ann.Loraine@uncc.edu>
cc: "ktsuttlemyre@gmail.com" <ktsuttlemyre@gmail.com>
date: Wed, Apr 30, 2014 at 10:07 AM
subject: RE: IGB problems

On second thought Joana, you should follow both sets of directions to be more thorough.

1. Step 1 (Clear IGB Cache)
Go to File > Preferences > Data Sources and click the 'Empty Cache' button at the bottom of the screen.
2. Step 2 (Reset Preferences)
Go to *File > Preferences > Other Options and click the 'Reset preferences to defaults' button at the bottom of the screen.

Best Regards,
-David

from: Norris, David <dcnorris@uncc.edu>
to: "JOANA.DE BRITO LOURENCO.SEQUEIRA MENDES.596874" <jsequeiramendes@cbm.csic.es>,
"Loraine, Ann" <Ann.Loraine@uncc.edu>
cc: "ktsuttlemyre@gmail.com" <ktsuttlemyre@gmail.com>
date: Wed, Apr 30, 2014 at 10:01 AM
subject: RE: IGB problems

I sent the wrong directions just now for clearing your preferences, please disregard and follow this instead.

Go to *File > Preferences > Other Options and click the 'Reset preferences to defaults' button at the bottom of the screen.

-David
---------------------------------------------------------------------------
David Norris | Senior Software Developer | Loraine Lab
UNC Charlotte | Dept. of Bioinformatics and Genomics
9201 University City Blvd. | Charlotte, NC 28223
dcnorris@uncc.edu | http://www.uncc.edu

from: Norris, David <dcnorris@uncc.edu>
to: "JOANA.DE BRITO LOURENCO.SEQUEIRA MENDES.596874" <jsequeiramendes@cbm.csic.es>,
"Loraine, Ann" <Ann.Loraine@uncc.edu>
cc: "ktsuttlemyre@gmail.com" <ktsuttlemyre@gmail.com>
date: Wed, Apr 30, 2014 at 9:58 AM
subject: RE: IGB problems

Hi Joana,
Could you try clearing your preferences as we discussed briefly in the meeting yesterday. (Go to File > Preferences > Data Sources and click the 'Empty Cache' button at the bottom of the screen.) It would be best to start with a clean slate since you have been experimenting so much in the past few days. After clearing your preferences and loading these files again please let us know if your problem occurs again. If you want to load any of your sessions, please use only the updated sanitized versions I have sent you this morning. Hope this help!

Best Regards,
David

---------------------------------------------------------------------------
David Norris | Senior Software Developer | Loraine Lab
UNC Charlotte | Dept. of Bioinformatics and Genomics
9201 University City Blvd. | Charlotte, NC 28223
dcnorris@uncc.edu | http://www.uncc.edu

from: JOANA.DE BRITO LOURENCO.SEQUEIRA MENDES.596874 <jsequeiramendes@cbm.csic.es>
to: "Loraine, Ann" <Ann.Loraine@uncc.edu>
cc: "ktsuttlemyre@gmail.com" <ktsuttlemyre@gmail.com>,
"Norris, David" <dcnorris@uncc.edu>
date: Wed, Apr 30, 2014 at 6:00 AM
subject: Re: IGB problems

Hi all,

yesterday I had lots of troubles again, just to load genome + 9 bed files (no gr files, just the colored boxes you saw the other day).
Everytime I opened it, all the removed servers were there again and I had to make many attempts to see something and eventually crashed again.

Today, the servers are OK everytime I open IGB (attached screenshot). However I load the At genome and after I try to load the files directly (not opening sessions just in case, as yesterday the servers would become enabled) and the bed files are opened but not loaded.
Internet connection is apparently ok.
This problem comes and goes... is it the server? Or even though connection is OK could be a problem here?

Thanks for your help,

In the meeting Ann had her clear out her bundle cache. I gave her a screenshot of the IGB default server list, a link to bedgraph and wig format specs, a link to tabix user manual and a tabix example from wiki.transvar

File Formats
http://genome.ucsc.edu/FAQ/FAQformat.html

Tabix Manual
http://wiki.transvar.org/confluence/download/attachments/30638181/tabix.1.pdf?version=1&modificationDate=1347445403000

Tabix Example
http://wiki.transvar.org/confluence/display/igbdevelopers/RNASeq+quickstart+-+from+sequences+to+alignments+to+visualization+in+IGB

from: Loraine, Ann <Ann.Loraine@uncc.edu>
to: "JOANA.DE BRITO LOURENCO.SEQUEIRA MENDES.596874" <jsequeiramendes@cbm.csic.es>
cc: "ktsuttlemyre@gmail.com" <ktsuttlemyre@gmail.com>,
"Norris, David" <dcnorris@uncc.edu>
date: Mon, Apr 28, 2014 at 12:43 PM
subject: Re: IGB problems

Do you have some time right now?

I will start a GoTo meeting and we can get going now if you have time.

This works best if you have headphones - just plug into your audio jack on
your computer.

Details:

1. Please join my meeting.
https://global.gotomeeting.com/meeting/join/319869997

2. Use your microphone and speakers (VoIP) - a headset is
recommended. Or, call in using your telephone.

United States:
+1 (646) 749-3112

Access Code:
319-869-997
Audio PIN: Shown after joining the meeting

Meeting ID:319-869-997

GoToMeeting
Online-Meetings made easy

from: JOANA.DE BRITO LOURENCO.SEQUEIRA MENDES.596874 <jsequeiramendes@cbm.csic.es>
to: "Loraine, Ann" <Ann.Loraine@uncc.edu>
cc: "ktsuttlemyre@gmail.com" <ktsuttlemyre@gmail.com>,
"Norris, David" <dcnorris@uncc.edu>
date: Mon, Apr 28, 2014 at 12:29 PM
subject: Re: IGB problems

Hi Ann,

since you told me that once, I already did it today. More than once, actually, as I am desperate!!
I'll do it again and send you the screenshots though. Here they go.

As for the meeting I would really appreciate that. How should we do it? I only have skype, but I can check the other one.

Thanks,

Joana

from: Loraine, Ann <Ann.Loraine@uncc.edu>
to: "JOANA.DE BRITO LOURENCO.SEQUEIRA MENDES.596874" <jsequeiramendes@cbm.csic.es>,
"ktsuttlemyre@gmail.com" <ktsuttlemyre@gmail.com>,
"Norris, David" <dcnorris@uncc.edu>
date: Mon, Apr 28, 2014 at 12:18 PM
subject: Re: IGB problems

Can you try this and let me know what happens?

Restart IGB.
Click ³Configure² (lower left corner of Data Access tab)
A new window will open.
Click Empty Cache (button at bottom of the screen)
And then please make a screen capture of this window and send it to me.

Also, do you have some time today to show us on your computer what is
going on? If you have time, we can set up a GoTo meeting and communicate
over the computer. (GoTo meeting is like Skype)

I¹m sorry for all the trouble!

-Ann