Difference between revisions of "JBrowse 2 Tutorial PAG 2022"

Revision as of 23:45, 28 December 2021

This is very much a draft version of the PAG 2022 tutorial, using the JBrowse 1 tutorial as a template.

This tutorial assumes a VirtualBox Ubuntu 18.04 (LTS) instance with the tutorial bundle zip file, also available on Amazon S3: JBrowse PAG 2020.ova (about 4GB) or PAG_2020_JBrowse.zip (about 36MB) for just the JBrowse source and data files for this tutorial.

Prerequisites

JBrowse 2 is both a desktop and server application. In this tutorial, we will focus on the desktop application to make our lives easier, but the server application is pretty easy to set up and has simple prerequisites (but reminder, you don't need this for this tutorial):

• a web server like Apache or Nginx
• NodeJS version 10 or better

That's really it for the server. Other things the would likely help include GenomeTools for sorting GFF, SamTools for working with BAM and CRAM files, and tabix for indexing various file.

But, again, none of those things are needed today!

JBrowse Introduction

How and why JBrowse 2 is different from most other web-based genome browsers, including JBrowse and GBrowse.

Replace with current presentation!

Setting up JBrowse

Getting JBrowse

A Short Detour for GFF

GFF (Generic Feature Format) is a very commonly used text format for describing features that exist on sequences. We'll head off to that page to talk about it a bit.

Features from a directory of files

Here, we'll use the Bio::DB::SeqFeature::Store adaptor in "memory" mode to read a directory of files. There are adaptors available for use with many other databases, such as Chado and Bio::DB::GFF.

Config file: pythium-1.conf

{
  "description": "PAG 2017 P. ultima Example",
  "db_adaptor": "Bio::DB::SeqFeature::Store",
  "db_args" : {
      "-adaptor" : "memory",
      "-dir" : ".."
   },
...

Specify reference sequences

Load Feature Data

Index feature names

Features from GFF3 or BED files

Quantitative data

Changing the way tracks look

Using Plugins

Other links