Missing features in Jbrowse

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Missing features in Jbrowse

Mariene Wan

Hi,


I'm using InterMine version 1.8.5.

I configured the integrated JBrowse into my InterMine. The problem is that i'm not seeing the correct features numbers on the JBrowse.

I've got the correct number of features into my InterMine instance but not in the integrated JBrowse (just a few of them).



Where are stored the JBrowse data ? I'm not able to check any log so I'm a bit stuck. To be honest I don't really understand how does the integrated JBrowse work.



Many thanks,


Best regards,


Mariene


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Re: Missing features in Jbrowse

sergio contrino-2
dear Mariene,
thank you for getting in touch.
do you mean you have installed your jbrowse server for your intermine,
following
https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse
?
if so, please check that you are pointing to the webservices of your
mine in your jbrowse configuration
please let us know if you have still problems (or if i misunderstood the
problem)
thanks!
sergio


On 13/06/2019 16:48, Mariene Wan wrote:

> Hi,
>
>
> I'm using InterMine version 1.8.5.
>
> I configured the integrated JBrowse into my InterMine. The problem is
> that i'm not seeing the correct features numbers on the JBrowse.
>
> I've got the correct number of features into my InterMine instance but
> not in the integrated JBrowse (just a few of them).
>
>
>
> Where are stored the JBrowse data ? I'm not able to check any log so I'm
> a bit stuck. To be honest I don't really understand how does the
> integrated JBrowse work.
>
>
>
> Many thanks,
>
>
> Best regards,
>
>
> Mariene
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: Missing features in Jbrowse

Mariene Wan
Dear Sergio,

thank you for your answer.

I checked my web.properties file and I'm pointing on the right webservice. (I followed the documentation you mentionned).

I attached a screenshot showing the JBrowse and the dev mod of my browser. The thing is I'm supposed to see more "consensus copies" that I'm currently seeing and I see no errors in the debug console, so I don't know where I'm supposed to go to fix this error or at least to see an error message. In my example, I have ~250 consensus copies (these copies are present in my InterMine instance and in the InterMine database (I checked) but I'm seeing only half of them on the JBrowse.

Thank you for your help,

Best regards,

Mariene



________________________________________
De : sergio contrino <[hidden email]>
Envoyé : jeudi 13 juin 2019 18:00
À : Mariene Wan; [hidden email]
Objet : Re: [InterMine Dev] Missing features in Jbrowse

dear Mariene,
thank you for getting in touch.
do you mean you have installed your jbrowse server for your intermine,
following
https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse
?
if so, please check that you are pointing to the webservices of your
mine in your jbrowse configuration
please let us know if you have still problems (or if i misunderstood the
problem)
thanks!
sergio


On 13/06/2019 16:48, Mariene Wan wrote:

> Hi,
>
>
> I'm using InterMine version 1.8.5.
>
> I configured the integrated JBrowse into my InterMine. The problem is
> that i'm not seeing the correct features numbers on the JBrowse.
>
> I've got the correct number of features into my InterMine instance but
> not in the integrated JBrowse (just a few of them).
>
>
>
> Where are stored the JBrowse data ? I'm not able to check any log so I'm
> a bit stuck. To be honest I don't really understand how does the
> integrated JBrowse work.
>
>
>
> Many thanks,
>
>
> Best regards,
>
>
> Mariene
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org

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jbrowse.png (445K) Download Attachment
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Re: Missing features in Jbrowse

Mariene Wan
Hi,

I tried to find out where my problem comes from and I found nothing.

After integrating the data provided in the input file (file_annotated_copies), there were some missing copies that are not showing up in intermine JBrowse but they exist in intermine's database (e.g: "ms70542_scaffold_203_DHX-comp_Alyr_TEdenovoGr-B-G4126-Map20_reversed"). I also noticed that the file downloaded from JBrowse (Consensus copy-...) doesn't contain the missing copies.

I verified the intermine DB and the copies were there.

Something happens while loading/showing the data in JBrowse and I'm trying to figure it out.

Please see the attached screenshots for more details.

Best regards,

Mariene
________________________________________
De : Mariene Wan
Envoyé : lundi 17 juin 2019 11:01
À : sergio contrino; [hidden email]
Objet : RE: [InterMine Dev] Missing features in Jbrowse

Dear Sergio,

thank you for your answer.

I checked my web.properties file and I'm pointing on the right webservice. (I followed the documentation you mentionned).

I attached a screenshot showing the JBrowse and the dev mod of my browser. The thing is I'm supposed to see more "consensus copies" that I'm currently seeing and I see no errors in the debug console, so I don't know where I'm supposed to go to fix this error or at least to see an error message. In my example, I have ~250 consensus copies (these copies are present in my InterMine instance and in the InterMine database (I checked) but I'm seeing only half of them on the JBrowse.

Thank you for your help,

Best regards,

Mariene



________________________________________
De : sergio contrino <[hidden email]>
Envoyé : jeudi 13 juin 2019 18:00
À : Mariene Wan; [hidden email]
Objet : Re: [InterMine Dev] Missing features in Jbrowse

dear Mariene,
thank you for getting in touch.
do you mean you have installed your jbrowse server for your intermine,
following
https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse
?
if so, please check that you are pointing to the webservices of your
mine in your jbrowse configuration
please let us know if you have still problems (or if i misunderstood the
problem)
thanks!
sergio


On 13/06/2019 16:48, Mariene Wan wrote:

> Hi,
>
>
> I'm using InterMine version 1.8.5.
>
> I configured the integrated JBrowse into my InterMine. The problem is
> that i'm not seeing the correct features numbers on the JBrowse.
>
> I've got the correct number of features into my InterMine instance but
> not in the integrated JBrowse (just a few of them).
>
>
>
> Where are stored the JBrowse data ? I'm not able to check any log so I'm
> a bit stuck. To be honest I don't really understand how does the
> integrated JBrowse work.
>
>
>
> Many thanks,
>
>
> Best regards,
>
>
> Mariene
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

files.png (1M) Download Attachment
Consensus copy-DHX-comp_Alyr_TEdenovoGr-B-G4126-Map20_reversed-1..5085(1).gff3 (47K) Download Attachment
copy_info.png (64K) Download Attachment
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Re: Missing features in Jbrowse

sergio contrino-2
dear Mariene,
thank you for the further info. we will check it hopefully tomorrow.
are your intermine and jbrowse instances available to the
public/reachable, so we can have a look directly?
thanks
sergio

On 24/06/2019 15:18, Mariene Wan wrote:

> Hi,
>
> I tried to find out where my problem comes from and I found nothing.
>
> After integrating the data provided in the input file (file_annotated_copies), there were some missing copies that are not showing up in intermine JBrowse but they exist in intermine's database (e.g: "ms70542_scaffold_203_DHX-comp_Alyr_TEdenovoGr-B-G4126-Map20_reversed"). I also noticed that the file downloaded from JBrowse (Consensus copy-...) doesn't contain the missing copies.
>
> I verified the intermine DB and the copies were there.
>
> Something happens while loading/showing the data in JBrowse and I'm trying to figure it out.
>
> Please see the attached screenshots for more details.
>
> Best regards,
>
> Mariene
> ________________________________________
> De : Mariene Wan
> Envoyé : lundi 17 juin 2019 11:01
> À : sergio contrino; [hidden email]
> Objet : RE: [InterMine Dev] Missing features in Jbrowse
>
> Dear Sergio,
>
> thank you for your answer.
>
> I checked my web.properties file and I'm pointing on the right webservice. (I followed the documentation you mentionned).
>
> I attached a screenshot showing the JBrowse and the dev mod of my browser. The thing is I'm supposed to see more "consensus copies" that I'm currently seeing and I see no errors in the debug console, so I don't know where I'm supposed to go to fix this error or at least to see an error message. In my example, I have ~250 consensus copies (these copies are present in my InterMine instance and in the InterMine database (I checked) but I'm seeing only half of them on the JBrowse.
>
> Thank you for your help,
>
> Best regards,
>
> Mariene
>
>
>
> ________________________________________
> De : sergio contrino <[hidden email]>
> Envoyé : jeudi 13 juin 2019 18:00
> À : Mariene Wan; [hidden email]
> Objet : Re: [InterMine Dev] Missing features in Jbrowse
>
> dear Mariene,
> thank you for getting in touch.
> do you mean you have installed your jbrowse server for your intermine,
> following
> https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse
> ?
> if so, please check that you are pointing to the webservices of your
> mine in your jbrowse configuration
> please let us know if you have still problems (or if i misunderstood the
> problem)
> thanks!
> sergio
>
>
> On 13/06/2019 16:48, Mariene Wan wrote:
>> Hi,
>>
>>
>> I'm using InterMine version 1.8.5.
>>
>> I configured the integrated JBrowse into my InterMine. The problem is
>> that i'm not seeing the correct features numbers on the JBrowse.
>>
>> I've got the correct number of features into my InterMine instance but
>> not in the integrated JBrowse (just a few of them).
>>
>>
>>
>> Where are stored the JBrowse data ? I'm not able to check any log so I'm
>> a bit stuck. To be honest I don't really understand how does the
>> integrated JBrowse work.
>>
>>
>>
>> Many thanks,
>>
>>
>> Best regards,
>>
>>
>> Mariene
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>>
>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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dev mailing list
[hidden email]
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Re: Missing features in Jbrowse

Rachel Lyne-2
In reply to this post by Mariene Wan
Dear Mariene,

We can't see anything obvious from the information you have sent us so
far.  Could you please send a few examples of some that do work and some
that don't?

Thanks,

Rachel.



On 2019-06-24 15:18, Mariene Wan wrote:

> Hi,
>
> I tried to find out where my problem comes from and I found nothing.
>
> After integrating the data provided in the input file
> (file_annotated_copies), there were some missing copies that are not
> showing up in intermine JBrowse but they exist in intermine's database
> (e.g:
> "ms70542_scaffold_203_DHX-comp_Alyr_TEdenovoGr-B-G4126-Map20_reversed").
> I also noticed that the file downloaded from JBrowse (Consensus
> copy-...) doesn't contain the missing copies.
>
> I verified the intermine DB and the copies were there.
>
> Something happens while loading/showing the data in JBrowse and I'm
> trying to figure it out.
>
> Please see the attached screenshots for more details.
>
> Best regards,
>
> Mariene
> ________________________________________
> De : Mariene Wan
> Envoyé : lundi 17 juin 2019 11:01
> À : sergio contrino; [hidden email]
> Objet : RE: [InterMine Dev] Missing features in Jbrowse
>
> Dear Sergio,
>
> thank you for your answer.
>
> I checked my web.properties file and I'm pointing on the right
> webservice. (I followed the documentation you mentionned).
>
> I attached a screenshot showing the JBrowse and the dev mod of my
> browser. The thing is I'm supposed to see more "consensus copies" that
> I'm currently seeing and I see no errors in the debug console, so I
> don't know where I'm supposed to go to fix this error or at least to
> see an error message. In my example, I have ~250 consensus copies
> (these copies are present in my InterMine instance and in the
> InterMine database (I checked) but I'm seeing only half of them on the
> JBrowse.
>
> Thank you for your help,
>
> Best regards,
>
> Mariene
>
>
>
> ________________________________________
> De : sergio contrino <[hidden email]>
> Envoyé : jeudi 13 juin 2019 18:00
> À : Mariene Wan; [hidden email]
> Objet : Re: [InterMine Dev] Missing features in Jbrowse
>
> dear Mariene,
> thank you for getting in touch.
> do you mean you have installed your jbrowse server for your intermine,
> following
> https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse
> ?
> if so, please check that you are pointing to the webservices of your
> mine in your jbrowse configuration
> please let us know if you have still problems (or if i misunderstood
> the
> problem)
> thanks!
> sergio
>
>
> On 13/06/2019 16:48, Mariene Wan wrote:
>> Hi,
>>
>>
>> I'm using InterMine version 1.8.5.
>>
>> I configured the integrated JBrowse into my InterMine. The problem is
>> that i'm not seeing the correct features numbers on the JBrowse.
>>
>> I've got the correct number of features into my InterMine instance but
>> not in the integrated JBrowse (just a few of them).
>>
>>
>>
>> Where are stored the JBrowse data ? I'm not able to check any log so
>> I'm
>> a bit stuck. To be honest I don't really understand how does the
>> integrated JBrowse work.
>>
>>
>>
>> Many thanks,
>>
>>
>> Best regards,
>>
>>
>> Mariene
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>>
>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev