W5. Preprocessing & Mapping

1. Quality control using FastQC

2. Read trimming using Sickle

3. Read alignment using STAR

(homework w5)

W8. Functional Enrichment

1. Gene ontology analysis

2. Gene set enrichment analysis

3. Deconvolution immune profile


W6. Transcriptome assembly

1. Understanding BAM format

2. Normal and reference-guided assembly using StringTie

(homework w6)


W7. Quantification &

Differential Expression

1. Normalization of count data

2. Quantification using FeatureCounts

3. DEG analysis using DESeq2

(homework w7)

W13. Data clustering

1. Non-negative matrix factorization

2. k-means clustering