Developed independently as part of coursework for Bioinformatics Programming and System Management at the University of Edinburgh. The original file containing a log of all the compressed FASTQ RNA-Seq files is included as Tco2.fqfiles, however the actual compressed FASTQ files are not included due to their size.
Pipeline taking Trypanosoma congolense RNA-Seq data in compressed FASTQ format. Runs a quality check on the data, aligns the read pairs to a Trypanosoma congolense genome (BAM format), generates count data of the number of reads that align to gene-coding regions of the genome, generates TXT files with average expression level per gene, after which the fold-change is calculated between chosen group-wise comaprisons.
Step by step instructions indicated in "Help_manual.pdf". Script files run Bash and are intended to be run on Linux.