This pipeline performs the initial RNAseq gene expression element of the horizontal transfer study.
We did PacBio sequencing after we had these RNAseq results. We were able to identify more informative sites using read variant phasing. Therefore the RNAseq analysis was updated to include the extra variants. Code to run the final analysis is in the "updated" folder.
There's no container for this analysis. Instead I set up a Micromamba environment, which
has installed featureCounts (from subread), DESeq and R and its required packages.
The requirements.txt file contains the list of packages and versions.