Project 3

Project 3: Implement a bioinformatic workflow to detect differential RNA splicing

Background

Many cancers are at least partly initiated by the expression of aberrant transcript isoforms. RNA-seq is often analyzed using known annotated isoforms but tumors can also express novel isoforms that can only detected using dedicated tools.

Data

• simple fastq file, available at https://github.com/IARCbioinfo/data_test

Requirements

• basic bash scripting (running a software in command line)
• nextflow programming (good understanding of practical 1)

Steps

1. download the https://github.com/IARCbioinfo/data_test
2. download and test software SUPPA2 (see documentation)
3. write a nextflow pipeline, following the IARCbioinfo template (IARCbioinfo/template-nf). The script would require (1) a process that trims reads, (2) a process to run RNA-seq quantification with salmon; (2) a process that runs SUPPA2.
4. Optional, if time left: running the script on an actual cancer case from SRA

Expected difficulties

• coding in Nextflow

Tips:

• look at examples of nextflow pipelines (e.g., IARCbioinfo/fastqc-nf), possibly using them as a starting point instead of doing it from scratch

Resources

• Nextflow documentation
• Practical 1
• Nextflow tutorial