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Learn Bioinformatics the Right Way (2019)

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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 Tests
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