Iso-Seq Browser

Iso-Seq Browser (ISB) is an interactive visual analytics tool for long-read RNA sequencing data produced by Pacific Biosciences’ isoform sequencing (Iso-Seq) techniques. Key features of ISB are: 1) an exon-only web-based interface with zooming and exon highlighting for exploring reference gene transcripts and novel gene isoforms, 2) automated grouping of transcripts and isoforms by similarity, 3) many customization features for data exploration and creating publication ready figures, and 4) exporting selected isoforms into fasta files for further analysis. ISB builds on the excellent MatchAnnot and Isoview tools, both of which provides analyses for Iso-Seq data.

ISB is written in Python and uses Conda for package management.

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Requirements

• Linux, Unix, or Mac OSX operating system with Make utility, which is included in all major distributions
• Miniconda, Python2 version for a minimalist Python installation or Anaconda, Python2 version for a complete scientific Python installation. Both Miniconda and Anaconda can be installed and used in a user's workspace, and neither requires any system-level permissions.

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Installation and running

1. Clone the repository:

   $ git clone https://github.com/goeckslab/isoseq-browser
   

   (or download and unzip form 'Clone or Download button'):

2. Run the Iso-Seq Browser:

   $ make run
   

   This will (i) create and populate a conda environment; (ii) download the required gene annotation and sample MCF7 dataset; and (iii) start ISB.

You can also issue four separate commands to set up and run ISB:

• Create the environment:

  $ make env
  

• Download a gene annotation and sample data:

  $ make gencode.v25.annotation.gtf
  $ make mcf7_matchAnnot_results_download.pickle
  

• Run Isoseq-browser:

   make run
  

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Using your own data

• Isoseq-browser requires two inputs: (a) a gene annotation in GTF format and (b) a MatchAnnot pickle file. Gene annotations are best found at GENCODE. Run MatchAnnot to create a pickle file with long reads matches to gene annotations. Here are instructions for running MatchAnnot.

• Run Isoseq-browser by specifying your own gene annotation and pickle file:

   make run ANNOTATION_GTF=my_annotation.gtf MATCHES_INPUT=my_matchannot_results.pickle
  

  you can also enter your gene annotation and pickle file in the browser as well.

Tips

• Visualizing the first gene will take ~90 seconds because the annotation and pickle files need to be loaded into memory. Visualization additional genes will be instantaneous.
• Grouping isoforms into many (> 10) clusters can be quite slow.

Reference

• Hu, Jingyuan, Prech Uapinyoying, and Jeremy Goecks. "Interactive analysis of Long-read RNA isoforms with Iso-Seq Browser." bioRxiv (2017): 102905.