Re: [Gmod-ajax] Jbrowse2 chunksize error on upload of gff3 file.

[Adams, S. <Sal...@wa...>]

Dear Colin,

Thanks for getting back to me so quick. I must admit to being rather smitten with JBrowse2. We work with only recently described nematodes and I think this will be a great way of sharing our data with collaborators etc. I am going to check out your suggestions now.

Thanks again

Sally
________________________________
From: Colin <col...@gm...>
Sent: 09 December 2020 23:04
To: Adams, Sally <Sal...@wa...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] Jbrowse2 chunksize error on upload of gff3 file.

Hi there,
Really glad to hear interest in JBrowse 2 :)


In general these chunkSizeLimits are a pain and we are working to solve them

References
https://github.com/GMOD/tabix-js/issues/120
https://github.com/GMOD/tabix-js/pull/117

These could help with this issue

In general, these error messages may also happen if you are zoomed too far out. We are trying to put a heuristic that says "Zoom in to see features" or something like this also in jbrowse 2, but this is not available
Reference for that issue
https://github.com/GMOD/jbrowse-components/pull/1394

If you zoom in and hit the "Reload" button, the "chunkSizeLimit" error might go away

-Colin

On Wed, Dec 9, 2020 at 5:27 PM Adams, Sally <Sal...@wa...<mailto:Sal...@wa...>> wrote:
Hi there,

I am in the process of annotating my Genome using Maker2 and would like to use Jbrowse2 to visually inspect the annotation. I have been following the method outlined at https://jbrowse.org/jb2/docs/combined/
JBrowse 2 combined guide | JBrowse<https://jbrowse.org/jb2/docs/combined/>
This document is a collection of all our documentation. It includes our quick start guide, user guide, configuration guide, CLI guide, developer guide, and FAQ. You can browse the other documents individually, but this page is to help simple ctrl+f searching and easy browsing. You can also download a pdf version of these same docs located at https://jbrowse.org/jb2/jbrowse2.pdf
jbrowse.org<http://jbrowse.org>
I downloaded using the CLI and have successfully uploaded both the genome and a vcf file. It looks great. However, I am having trouble with the gff3 file. I have followed the sorting, compression and tabix indexing steps but I keep getting the error that the chunk size is too large (mine is nearly 4 million and my chunk size is set at 2 million). I know in Jbrowse you can reset the chunk size but I am really unsure where I might be able to set this in the config files for Jbrowse2. I know my gff file is pretty big as it contains the annotated repeats as well as predicted genes. Am I asking for too much?

Thanks ever so much

Sally
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