Practicals of Bioinformatics

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Practicals of bioinformatics – Syllabus

Course Information – Fall 2019

Postgraduate program in Biological Sciences, UNAM

64 hours

GitHub repository (in Spanish)

Instructors
Camille Truong, UNAM

Alicia Mastretta Yanes, CONABIO

Rodolfo Ángeles Argáiz, UNAM

Location & Time
CONABIO, Monday/Wednesday 15:00PM-18:00AM

Objectives

Students with a background in bioinformatics will address issues related to deep sequencing data analysis for their thesis project. They will present a methodological problem, collaborate in the review of other student's code, and participate in theoretical-practical discussions. Specifically, students will:

Learn to build efficient scripts, loops and pipelines
Organize and document their bioinformatic project in GitHub and OSF using version control
Discuss and resolve bioinformatic problems relevant to their project
Receive and provide feedback to other student's code

Prerequisites
Having successfully completed a bioinformatic introductory course covering bash, R and/or python, or with mid-level bioinformatic

skills: Navigating fluently through a file system using the command line; being able to read, make and adapt your own scripts.
Having deep sequencing data from their thesis project at the beginning of the course.

Topics covered
UNIT 1 – Reproducibility and documentation of bioinformatics analysis
1.1. The reproducibility crisis in science and how to fight it

1.2. Data organization

1.3. Scripts organization

1.4. Introduction to GitHub and OSF

1.5. Version control

UNIT 2 – Best practices for writing and documenting scripts
2.1. Working directory, absolute and relative paths

2.2. Use of variables and wildcards

2.3. When and how to use them for loops

2.4. Tips and tricks on the terminal and the text editor

UNIT 3 – Discussion of bioinformatic methods applied to different data types
3.1. Quality evaluation, denoising and demultiplexing

3.2. Fractional genome sequencing (RAD, GBS)

3.3. Whole genome sequencing

3.4. Transcriptomics

3.5. Meta-barcoding

UNIT 4 – Collaborative work on bioinformatic scripts
4.1. Create and manage your bioinformatic project

4.2. Use GitHub and OSF to handle collaborative work

4.3. Receive and provide feedback from other students

Evaluation
Presentation of the student project with a focus on bioinformatic methods (in English) – 5%

Presentation of the student Github repository, including documentation and tasks written in English – 5%

Presentation of a bioinformatic issue related to the project, i.e. how to perform a loop, design an efficient pipeline or optimally choose parameters. The presentation should include: brief background, description of the problem, expected output, scripts and outputs attempted so far. Each student will present at least 3 scheduled problems – 30%

Participation in class – 15%

Feedback to other student's code (in class and in GitHub) – 15%

Seminar on a methodological topic (in English) – 10%

Evaluation of the student GitHub repository. Two revision dates: October 30 (comments are made) and November 20 (final delivery with comments resolved) – 20%

Bibliography

Buffalo V (2015) Bioinformatics data skills. O'Reilly Media.

Grolemund G (2014). Hands-on programming with R. O'Reilly Media.

Haddock SHD, Dunn CW (2011) Practical computing for biologists. Sinauer Associates Sunderland.

Gondro C (2015) Primer to analysis of genomic data using R. Springer.