1. Check the quality of the raw sequencing data (QC report) using:

• FastQC
• MultiQC

2. Pre-processing

1. Remove reads containing adapters using Cutadapt
2. Remove reads containing N > 10% (N represents base that could not be determined)
3. Remove reads where the Qscore (Quality value) of over 90% bases of the read is <= 10

3. Align reads to a reference using STAR

4. Count the number of reads assigned to each contig/gene using featureCounts (a part of RSubread package)

• Extract counts and store in a matrix
• Create column metadata (sampleinfo) table

6. Analyze count data using DESEQ2