This course contains materials for BMMB 852: Applied Bioinformatics course offered in the Fall of 2019 at the Pennsylvania State University.
Dates: Aug 26th - December 13th, 2019
Lectures will appear as they are presented in class.
Lecture | Your Score |
---|---|
Lecture 1: Introduction to Bioinformatics
The one where we talk about what bioinformatics is and how to set up your computer. |
|
Lecture 2: The UNIX command line
The one where we talk about Unix and why you need to use it to make the most out of your data |
|
Lecture 3: Data Analysis with Unix
The one where I have an epiphany about data formats. Then, eventually we perform some data analysis. |
|
Lecture 4: What do the words mean
The one where we talk about why it is important to use the right words to describe biological concepts. |
|
Lecture 5 and 6: How to interpret the results produced by algorithms
The one where we talk about how functional annotation data is represented and how interpret a list of genes using that data |
|
Lecture 7 and 8: Biological data, their formats, habits and where to find them
The one where to talk about data types and describe the taming and care of FASTA, FASTQ and other beasts |
|
Lectures 9 and 10: Automating data access
The one where we talk about accession numbers and automating data download with efetch, and easearch |
|
Lectures 11 and 12: Quality Control of Sequencing Data
The one where we talk about writing scripts and introduce the FastQC tool. |
|
Lecture 13: Sequencing concepts
The one where we talk about single-end and and paired-end sequencing, pet peeves and how to compute sequencing coverages |
|
Lecture 14: Programming survival kit
The one where we learn the defense against the dark arts with charms and protection wards that keep evil at bay. |
|
Lecture 15 and 16: Sequence Alignments
The one where we talk about what an alignment is, what it means and which parameters govern which alignments are pfound |
|
Lecture 17 and 18: Basic Local Alignment Search Tool (BLAST)
The one where we talk about how BLAST works, how to run it both as a webserver and at the command line |
|
Lecture 19 and 20: Short Read Aligners
The one where we learn about high troughput sequence alignment of the short reads. |
|
Lecture 21 and 22: Visualizing and interpreting BAM files
The one where we look at BAM files via IGV and at the command line |
|
Lecture 23 and 24: Alignment formats: SAM and BAM. Filtering BAM files.
The one where we learn about all the information crammed into a format that is half genius, half tedious with a little insanity sprinkled in the middle. |
|
Lecture 25 and 26: Variation calling
The one where we learn about calling short variations and the VCF format. |
|
Lecture 27 and 28: RNA-Seq data analysis
The one where we learn how to quantify with sequencing |