Re: Questions on uploading tracks to Apollo

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Re: Questions on uploading tracks to Apollo

nathandunn




On Oct 17, 2020, at 7:55 AM, Abhijit Sanyal <[hidden email]> wrote:

Sure Nathan. No problem. I have another question for you.

 The admin at our institution installed Apollo via docker. But does not know where to look for the jbrowse scripts for loading the gff3 data. I see two folders created. 

docker-apollo/ and compose-apollo/

Which should I take to search for the scripts? I can send you screen shots if you want.

Thanks
Abhijit


I would just install JBrowse and use the scripts from that if possible.  Should be in the bin directory. 

You have a few options:

1 - install jbrowse directly from a download and use what is in the bin directory

2 - install jbrowse via docker: https://hub.docker.com/r/gmod/jbrowse

3 - use what is in the docker Apollo: /var/lib/tomcat9/webapps/ROOT/jbrowse/bin 

. . you would have the mount the directory in the case of 2 or 3 to use it externally






On Sat, Oct 17, 2020 at 8:19 PM Nathan Dunn <[hidden email]> wrote:
Do you mind if I reply to this on the Apollo groups so that others may benefit from our conversation?

Nathan

> On Oct 17, 2020, at 6:05 AM, Abhijit Sanyal <[hidden email]> wrote:
>
> 
> Hi Nathan,
>
> Just a few questions regarding upload of tracks to Apollo from the desktop
>
> 1) I have gff3 files to upload, however the options I see are "GFF3 JSON", "GFF3 JSON CANVAS", "GFF3", "GFF3 Canvas". Which one should I pick? I could not find a help page on this. Maybe I missed something?

I would use GFF3 to start (you can always delete or add with a different type later). 

The different types are referenced badly here. 


GFF3 uses the native GFF3 adapter, whereas JSON uses the “flatfile-to-json.pl” which would be recommended for long and dense GFF3 tracks, converting it into a modified file format with histograms.  

>
> 2) What does the "category" field stand for? I do not know what to put here.

You can leave this blank.  If you want a “section” in our track you put something in here: 


>
> 3) I have the following types of gff3 files for genes, repeats, ncRNA. For genes I will use "--type mRNA". What to use for the other two?
>


I would use whatever is in column 3 that you want to see, which is what it does the filter be.   Sometimes I have to play with it a bit to see what I want.  

The JBrowse community and doc might be helpful here as well.  


Sample files would help here if you can’t make this work. 

Hope all this helps. 

Nathan


> Thanks
> Abhijit

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