Class Schedule

Pre-Class

• Set up your TSCC account

  • Intructions here

• Practice Python on DataCamp

  • Website here

Sep 23 (Mon) 9am – 1pm

Intro to Sequencing, Unix, Data Download, Fastqc, STAR alignment

• Notebooks -TSCC login and Downloads -Data downloads and quality checks -STAR index and alignment

• Tutorials -Intro to bash commands -Set up Jupyter Notebooks -TSCC Job submission

• Lecture -Intro to Sequencing

Sep 24 (Tue) 9am – 1pm

Intro to Alignment, Submitting Jobs to Cluster, Samtools, and Gene quantification

• Notebooks -FeatureCounts -Samtools -Python demo - Counts and Conditions

• Tutorials -FeatureCounts tutorial -Samtools sort and indexing -Intro to Python -TPM and plotting demo

• Lecture

Sep 25 (Wed) 9am – 1pm

Differential Expression and GO Term Analysis

• Notebooks -Functions example RPKM and TPM -Plotting in python -DESeq2 Analysis

• Tutorials -DESeq2 Installs -Intro to PCA -Piping commands with bioinformatics tools

• Lecture

Oct 2 (Wed) 9am – 1pm

Python and Data Visualization and Group Presentations

-Notebooks -

-Tutorials

Office Hours

On Slack

---

Group Project

Project description: In your groups find a published RNA-seq data set. Use the skills you learned in class to process and analyze the data. Tell us what the results tell us about the biological question.

In your write up answer: Where is this dataset from? What question were they answering in this experiment? List the commands you used to process it. Plot ..... and give us those things.

---

Additional resources for bioinformatics: