Download ~5M Human RNA-Seq fragements from the SRA. Link to the suggested data: https://www.ncbi.nlm.nih.gov/sra/?term=SRR8797509
- Construct 5 Samples, each sample contains two parts.
- Part 1: 1M reads from the main reads file. (split the main file into 5 parts)
- Part 2: Shuffle the main reads file, and take random 1M Reads. (split the shuffled file into 5 parts)
- Example: Sample 1 will be divided into S1_1 & S1_2, unshuffled and shuffled, respectively.
- For Sample 1 only, use FASTQC to report the difference between S1_1 and S1_2
- For All Samples , Apply:
- Mild Trimming for SX_1. {shuffled}
- Aggressive Trimming for SX_2. {unshuffled}
- Align all the samples (1:5) using BWA and Hisat against the human reference file.
- BWA for SX_1 and HISAT for SX_2
- Export some useful statistics report for each sample indvidually.
- Apply reference-based trasncriptome assembly using stringTie.
- Step1. For the 5 samples unshuffled.
- Step2. For the 5 samples shuffled.