This repository contains scripts used to build compendia of publicly available RNAseq data for Pseudomonas aeruginosa.

The construction and composition of these compendia is documented in Doing et al. 2022.

Required input files and the main output files like raw and normalized compendia are stored on OSF: https://osf.io/s9gyu/

The compendia were originally constructed using a collection of bash, python, and R scripts which are documented in compendia_construction. This pipeline required a pre-downloaded SRA run table which was used to download FASTQ files of RNAseq data using fasterq-dump. These files were then mapped against P. aeruginosa transcriptomes using salmon, and counts were post-processed in R and python.

To facilitate the addition of new RNAseq samples to the compendia, we have provided an automated pipeline that will process new SRA experiment accessions, add the new counts to the original raw compendia, and re-filter and re-normalize the compendia. This pipeline is provided in auto_add_to_compendia. This pipeline automates the bash, R, and python scripts provided in compendia_construction with minor modifications to the original code.

Please submit an issue to the issue tracker.

This is a proof-of-principle project that could help set the stage for a versatile, scaleable pipeline.

Georgia Doing (@georgiadoing), Taylor Reiter (@taylorreiter)

See the LICENSE file above.

Complete.

Please cite

Computationally efficient assembly of a Pseudomonas aeruginosa gene expression compendium Georgia Doing, Alexandra J. Lee, Samuel L. Neff, Jacob D. Holt, Bruce A. Stanton, Casey S. Greene, Deborah A. Hogan bioRxiv 2022.01.24.477642; doi: https://doi.org/10.1101/2022.01.24.477642