This folder contains scripts to download and format all RNA-seq metadata for an organism from NCBI Sequence Read Archive. To simplify the process, we have created a docker container with all pre-requisite software.
The following code finds all RNA-seq data for Bacillus subtilis and saves the data to the file Bacillus_subtilis.tsv. Note that the species name must be enclosed in quotes.
docker run --rm -it avsastry/get-all-rnaseq:latest "Bacillus subtilis" > Bacillus_subtilis.tsvLocal installation requires Entrez direct and Python 3.6 or higher with Pandas. These are included in the conda environment file in the home directory.
./download_metadata.sh "Bacillus subtilis" > Bacillus_subtilis.tsv