#rev project
The scripts assume the following directories exist:
- work (for intermediate analysis output)
- data (fastq files go here)
- out (for final output)
A script to run STAR aligner on .fastq files.
A simple script to check several housekeeping genes for reasonable output (i.e. no obvious annotation mixups or RNA-Seq breakdowns)
Analyze gr38 genome to break out regions exclusively exon, intron or mixed and count reads in each region for each sample.
Calculate differences between treatment and controls in the annotated regions and look for signficant differences.
Helper functions used in the analysis.