Topics Covered
- Experimental design: number of reads, pair end sequencing, benefits (e.g. Cost, inhouse)
- Data processing: data format, data QC, alignment, visualization/quantification, issues specific to RNA-seq (splicing)
Practical
- Sequencing Data Quality Check
- RNA-seq alignment using STAR
- Post-alignment quality assessment
- Visualization of alignment
- Gene/Transcript quantification using htseq and RSEM