Back-splice junction indexing and querying
BIQ is a tool for searching k-mers that span backsplice junctions (BSJs) in a large collection of RNA-Seq experiments. The main use case is to identify experiments in which a particular circular RNA, identified by its backsplice junction, is expressed. The method is described in the manuscript on bioRxiv.
BIQ builds on top of KIQ, a software for indexing and querying k-mers in sequencing data sets.
An example installation can be found at e-rna.org or at GitHub.
It contains three BSJ k-mer indexes:
- Drosophila melanogaster, 103 RNA-Seq datasets from Westholm et al 2014.
- Human, 386 SRA files from ENCODE (only total RNA-Seq).
- Human, 2652 SRA files from Solomon et al. 2016.
BIQ is a React app built with create-react-app, which requires Node.js to be installed.
Download:
git clone https://github.com/pmenzel/biq
cd biq
First install the required packages:
npm install
Run the app locally in the development mode:
npm start
Open http://localhost:3000 to view it in the browser.
For preparing the installation on a web server, first run
npm run build
and then copy content of the build/ folder to the web server.
BIQ accesses KIQ and the backsplice junction index through an HTTP
endpoint. The folder http_endpoints contains HTTP wrappers for PHP
and AWS Lambda that can be used to call KIQ. The URLs for these endpoints
can be set in src/conf.js.
The enumeration of BSJ k-mers from annotated transcripts and
their exons is done with the script scripts_ensembl/enumerate_BSJs.pl.
BIQ also needs a JSON file containing the 5' and 3' sequences of the exons,
which are used to create a query k-mer. This JSON file is created with the
script scripts_ensembl/exons2json.pl.
Copyright (c) 2018,2019 Peter Menzel pmenzel@gmail.com
See the file LICENSE.