This pipeline chains together tasks required to analyse RNA-seq and small RNA-seq datasets used in project035. It is not a general purpose pipeline, and as such some variables are hard-coded. It contains the necessary custom Python and R scripts written for the project. It relies heavily on the CGAT code collection and ruffus, the former is available here on GitHub: https://github.com/CGATOxford/cgat

Third party tool (including R packages) requirements:

• DESeq2
• gplots
• RColorBrewer
• ggplot2
• featureCounts v1.4.6

Prior read QC and mapping was carried out using the CGATPipelines, pipeline_readqc.py and pipeline_mapping.py found in the CGATPipelines repo: https://github.com/CGATOxford/CGATPipelines

###Input The pipeline expects compressed alignment files (.bam), with files named according to the convention: condition-tissue-replicate.file_suffix

It also requires a gtf file of annotations of interest. These were either downloaded from ensembl, and processed directly using the CGATPipelines script pipeline_annotations.py (protein-coding genes and miRNAs), or converted from .bed format using the script bed2gff.py in the CGAT scripts repo.

For pipeline use instructions see the wiki.