nbutter/star repository overview

⁠RNASeq_FASTQ-Counts

Docker/Singularity container for workflow of pre-processing steps (fastq.gz to bam file format) required for a typical RNA sequencing experiment for transcriptome profiling or differential expression for species with an available reference genome.

⁠A few examples

To build with docker, change into the directory with the "Dockerfile" and execute: sudo docker build -t star .

Then run with docker using: docker run star STAR

Or to run the dockerhub version directly: docker run nbutter/star STAR

To build the docker image with singularity use: sudo singularity build star.sif docker://nbutter/star

Or if you want to build the local singularity image use: sudo singularity build star.sif star.build

To run the docker contianer with singularity use: singularity exec docker://nbutter/star STAR

Or to run your locally built singularity image use: singularity exec star.sif STAR

If you have used this work, you must acknoledge SIH, e.g: "The authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney."