petadimensionlab/docker_rnaseq_star repository overview

⁠Docker_STAR

RNAseq(STAR) analysis for docker.

Reference URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631051/⁠

⁠Usage

⁠Docker pull image

docker pull petadimensionlab/docker_rnaseq_star

⁠Docker run

docker run -it --name container_name -v /yourlocal_dir:/condir --rm  petadimensionlab/docker_rnaseq_star

Copy your local "genome file", "annotation file" and "sample ID file(fastq_files.txt)" into "/yourlocal_dir".

⁠Run this docker python script

⁠1.Download sras

# cd script
# python exec_download_sras.py

⁠2.Make STARindex

# python exec_make_STARindex.py

line 5 or 6 = Change the 'species'.

⁠3.Run RNAseq(STAR) analysis

# python  seq_exec_sra2readcount_STAR.py

line 3 to 15 = Change these as needed.

⁠Exit docker

# exit

⁠Caution

Need to limit the resource available to docker engine.

Reference URL:https://docs.docker.com/docker-for-mac/⁠

⁠Docker-compose

The dockercompose version is on Github here⁠.