[Gmod-ajax] problem with JBrowse

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[Gmod-ajax] problem with JBrowse

Putu Ayu G Sudyanti

Hello, 


I am trying to use JBrowse on my bam files with no success.  Based on the tutorial, I clicked on track, selected my .bam and .bai files and then clicked open after choosing Alignment2. I see the title of the newly created track but nothing else showed up. My bam files is sorted by left most coordinate as suggested on GMOD wiki. 


This is the first time I have used JBrowse so I am not sure what I am doing wrong. 


Any help would be appreciated. 


Thank you, 


Ayu 


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Re: problem with JBrowse

Scott Cain
Hi  Ayu,

The most common problem in situations like this is that the name of the reference sequence in JBrowse doesn't agree with the name of the reference sequence in the BAM file.  For example, you could have "ChrI" in JBrowse, but "Chr1" or "1" or "I" in the BAM file.  If those don't agree, then JBrowse doesn't understand that they go together.

If that isn't the problem, it would be helpful if you open the javascript console in your browser and copy and paste any error message that appear there when you try to load the BAM file.

Scott


On Sun, Oct 16, 2016 at 3:38 PM, Putu Ayu G Sudyanti <[hidden email]> wrote:

Hello, 


I am trying to use JBrowse on my bam files with no success.  Based on the tutorial, I clicked on track, selected my .bam and .bai files and then clicked open after choosing Alignment2. I see the title of the newly created track but nothing else showed up. My bam files is sorted by left most coordinate as suggested on GMOD wiki. 


This is the first time I have used JBrowse so I am not sure what I am doing wrong. 


Any help would be appreciated. 


Thank you, 


Ayu 


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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: problem with JBrowse

Scott Cain
Hi Ayu,

Please always reply on the mailing list so others have a chance to answer (who might know better than me!) and so the responses can be archived for future users.

The desktop application cannot share anything, since that would require a webserver.  You might be able to get the desktop application all configured the way you like and with data added and then package it up and send to your collaborators, but I really don't know what would be involved in doing that.

Possibly a better scenario would be to set up JBrowse in the typical way with a web browser and then password protect it with apache.  I haven't personally done that before either but I'm sure there are examples on the web describing how to do it.  Of course, how much work you'd need to put in to it also depends on how secure you need it to be.  Any BAM or BigWig files would need to be web accessible in some public way too, but it could be placed in a obfuscated URL to make it much less likely for somebody to stumble upon it.

Scott



On Wed, Oct 26, 2016 at 10:54 AM, Putu Ayu G Sudyanti <[hidden email]> wrote:

Hello Dr. Cain, 


Thank you so much for the help. I have succeeded in uploading my bam file with the correct reference genome. However, I managed to do this on the JBrowse desktop but not on the browser webpage. My end goal is to be able to store the data privately and share the link to my collaborator. Is this feasible in JBrowse? I know that on the top right hand corner of the webpage on SGD JBrowse there is a share link button but I cannot find the same one on the JBrowse desktop. 


Any help would be much appreciated. 


Thank you so much, 


Ayu 


From: Scott Cain <[hidden email]>
Sent: Sunday, October 16, 2016 7:05:46 PM
To: Putu Ayu G Sudyanti
Cc: [hidden email]
Subject: Re: [Gmod-ajax] problem with JBrowse
 
Hi  Ayu,

The most common problem in situations like this is that the name of the reference sequence in JBrowse doesn't agree with the name of the reference sequence in the BAM file.  For example, you could have "ChrI" in JBrowse, but "Chr1" or "1" or "I" in the BAM file.  If those don't agree, then JBrowse doesn't understand that they go together.

If that isn't the problem, it would be helpful if you open the javascript console in your browser and copy and paste any error message that appear there when you try to load the BAM file.

Scott


On Sun, Oct 16, 2016 at 3:38 PM, Putu Ayu G Sudyanti <[hidden email]> wrote:

Hello, 


I am trying to use JBrowse on my bam files with no success.  Based on the tutorial, I clicked on track, selected my .bam and .bai files and then clicked open after choosing Alignment2. I see the title of the newly created track but nothing else showed up. My bam files is sorted by left most coordinate as suggested on GMOD wiki. 


This is the first time I have used JBrowse so I am not sure what I am doing wrong. 


Any help would be appreciated. 


Thank you, 


Ayu 


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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: problem with JBrowse

Keiran Raine
Hi Ayu, Scott,

If you configure the server for password protection it should also be protecting the BAM/BigWig data under the same authentication method providing you serve the data from the same service.

I've only done this under HTTP_BASIC with LDAP authentication using Nginx (documented here), but for arbitrary user name password its pretty straight forward:

https://www.digitalocean.com/community/tutorials/how-to-set-up-password-authentication-with-nginx-on-ubuntu-14-04

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

On 26 Oct 2016, at 16:08, Scott Cain <[hidden email]> wrote:

Hi Ayu,

Please always reply on the mailing list so others have a chance to answer (who might know better than me!) and so the responses can be archived for future users.

The desktop application cannot share anything, since that would require a webserver.  You might be able to get the desktop application all configured the way you like and with data added and then package it up and send to your collaborators, but I really don't know what would be involved in doing that.

Possibly a better scenario would be to set up JBrowse in the typical way with a web browser and then password protect it with apache.  I haven't personally done that before either but I'm sure there are examples on the web describing how to do it.  Of course, how much work you'd need to put in to it also depends on how secure you need it to be.  Any BAM or BigWig files would need to be web accessible in some public way too, but it could be placed in a obfuscated URL to make it much less likely for somebody to stumble upon it.

Scott



On Wed, Oct 26, 2016 at 10:54 AM, Putu Ayu G Sudyanti <[hidden email]> wrote:

Hello Dr. Cain, 


Thank you so much for the help. I have succeeded in uploading my bam file with the correct reference genome. However, I managed to do this on the JBrowse desktop but not on the browser webpage. My end goal is to be able to store the data privately and share the link to my collaborator. Is this feasible in JBrowse? I know that on the top right hand corner of the webpage on SGD JBrowse there is a share link button but I cannot find the same one on the JBrowse desktop. 


Any help would be much appreciated. 


Thank you so much, 


Ayu 


From: Scott Cain <[hidden email]>
Sent: Sunday, October 16, 2016 7:05:46 PM
To: Putu Ayu G Sudyanti
Cc: [hidden email]
Subject: Re: [Gmod-ajax] problem with JBrowse
 
Hi  Ayu,

The most common problem in situations like this is that the name of the reference sequence in JBrowse doesn't agree with the name of the reference sequence in the BAM file.  For example, you could have "ChrI" in JBrowse, but "Chr1" or "1" or "I" in the BAM file.  If those don't agree, then JBrowse doesn't understand that they go together.

If that isn't the problem, it would be helpful if you open the javascript console in your browser and copy and paste any error message that appear there when you try to load the BAM file.

Scott


On Sun, Oct 16, 2016 at 3:38 PM, Putu Ayu G Sudyanti <[hidden email]> wrote:

Hello, 


I am trying to use JBrowse on my bam files with no success.  Based on the tutorial, I clicked on track, selected my .bam and .bai files and then clicked open after choosing Alignment2. I see the title of the newly created track but nothing else showed up. My bam files is sorted by left most coordinate as suggested on GMOD wiki. 


This is the first time I have used JBrowse so I am not sure what I am doing wrong. 


Any help would be appreciated. 


Thank you, 


Ayu 


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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank" class="">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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