This repository contains the code for the manuscript: "Quantitative transcriptomics and epigenomics data-analysis: a primer" (in submission at Frontiers in Genetics)
The files in this repository are:
Acc_List.txt: list of accessions (indicated by sra run id).
Adapters.fa: adapter sequences to trim from RNA-seq data (based on fastq output).
DE_analysis.R: script for differetial expression analysis in R.
fastq2counts.bash: bash script for performing subsequent preprocessing, alignment and summarization steps.