This project aims to practice most of the technologies and software you've learned so far the course, starting from data download to annotation and differential expression.
- For each step, document your workflow and commands, scripts to reproduce the same expirement.
- Everything must be reported and documented on Github.
- Fork this project and start your start commiting.
- Create a file named
user_info.mdand write down your full name, alongside your Nile Universty email address and Student ID.
Download ~25M Human RNA-Seq reads from the SRA.
- Construct 5 Samples, each sample contains two parts
- Part 1: 1M unique reads from the main reads file.
- Part 2: Shuffle the main reads file, and take random 1M Reads.
- Example: Sample 1 will be divided into S1_1 & S1_2, Unique and Random selected after shuffeling respectively.
- For Sample 1 only, use FASTQC to report the difference between between S1_1 and S1_2
- For Sample 1 only, Apply:
- Mild Trimming for S1_1.
- Aggressive Trimming for S1_2
- Align all the samples (1:5) using BWA and Hisat against the human reference file.
- Export some useful statistics report for each sample indvidually.
- Apply reference-based trasncriptome assembly using stringTie.
- Step1. For the 5 samples (without shuffeling) parts.
- Step2. For the 5 samples (with shuffeling applied) parts.