Question 1

1. Try to create a shell file to understand how bash works.
   • Process
2. Creat Slurm File in Rivanna
   • Process
3. Write the code for Mapping (Hisat2)
   • Process
4. 原来可以 slurm interactive job （我真的无语了！！！！！！）
   • Process
5. Use Samtools to sort sam file and Calculate RPKM using stringtie
   • Process
6. Generating Expression Matrix
   • Process

Question 2

1. Map the raw sequencing reads to the human genome (bowtie2)
   • Process
2. Peak calling (detect genome-wide binding sites) using the mapping result (after filtering low quality read ) (macs2)
   • Process

Question 3

1. Quality of sequence reads ( fastqc )
   • code
   • meaning
2. Mappability
   • Code
   • Meaning
3. Replicate correlation (reproducibility)
   • RNA seq
   • Chip seq
4. Duplicate Rate
   • Code
   • Meaning