In this repository, I try to replicate the results of Rodriguez2017 entitled Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains in a smaller scale.
In their original study, 64 fastq files existed. Because of my hardware limitations, I decided to use a fraction of their data. I implemented a pipeline that differed from theirs to a great extent. I used SRA toolkit -> FastQC -> Trimmomatic -> HISAT2 -> featureCounts -> DEseq2 route.
The subset data was a collection of 8 fastq files four of which corresponded to CEN.PK - St4288 strain which was optimised for p-coumaric acid production. (Four samples of replicate #1 were selected.)
The other four fastq files were from CEN.PK - St4408 strain which was not optimised for p-coumaric acid production. (Four samples of replicate #1 were selected.)
The scripts ran completely fine, however, the list of differentially expressed genes (DEGs) resulted from my scripts differed to some extents from their results. I assume the differences stem from the fact that I only used a fraction of their sequence data.
The results of script.sh and Analysis.R is provided in the Expected_Results folder