NGI during Covid-19 outbreak

NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.

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RNA-fusion analysis

Runs with illumina RNA-Seq data. Aligns to the reference genome, gives QC metrics, predicted gene fusions and finishes with graphically visualised reports.

rnafusion is a bioinformatics best-practice analysis pipeline used on RNA-Seq data with the intention of localising and visualising fusion genes.
The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
The workflow is built on a list of curated tools such as Arriba, EricScript, and FusionCatcher.

When we run analysis

We run this analysis for RNA-seq projects where we have prepared the sequencing library in-house. If you have prepared a library yourself and we are just sequencing, please get in touch and mention that you would like us to run this analysis.

The analysis works with any of the species that have a reference genome available in AWS-iGenomes. If in doubt, please ask whether we can run the pipeline for you.

Input data

bcl2fastq demultiplexed FastQ files and a genome reference.

Results

Depending on the tools specified, the pipeline generates text files with all the predicted gene fusions, BAM-alignment files and visualised reports in HTML-format.

Applications
Method Status

Pilot

We are currently testing this method. Please contact us to find out more.

Keywords