Bioinformatics Training Materials
On this page you will find a variety of curated training materials and tutorials related to bioinformatics, biostatistics, and general computational biology. They are broken down into two groups:
General Tutorials
- Introduction to the Unix Shell
- This tutorial is a modified form of the introduction to the Unix shell as offered by Software Carpentry. It focuses on teaching undergraduates the basic skills necessary to understand the shell and utilize command line tools.
- Key Skills: Unix, Bash, Command Line
- Introduction to Quality Assessment, FastQC, and Trimmomatic
- This tutorial is an introduction to the quality assessment step in a bioinformatics pipeline. It focuses on the most common file formats (FASTA/FASTQ), the motivation for and use of FastQC, and using Trimmomatic to trim paired-end reads. It is highly tailored to the use of the MDIBL Bioinformatics Core cluster to use example data.
- Key Skills: FastQC, Trimmomatic
- Introduction to TopHat
- This tutorial is an introduction to the TopHat2 software suite and its use in mapping RNA-seq reads. Though an incredible tool in any sequence analysis pipeline, this particular tutorial is highly tailored to the use of the MDIBL Bioinformatics Core.
- Key Skills: TopHat
- Introduction to HTseq
- This tutorial is an introduction to the
htseq-count function in the HTseq computational environment. Though useful in many situations, it is highly tailored to the use of the MDIBL Bioinformatics Core.
- Key Skills: HTseq, Samtools
- Introduction to NCBI and BLAST
- This tutorial was created for undergraduate students studying with Dr. Elizabeth Ehrenfeld at the Southern Maine Community College. It focuses primarily on learning how to navigate the NCBI website, perform simple queries, and understanding and perfomring BLAST alignments on simple sequences.
- Key Skills: BLAST, Entrez Search
- Converting a Genbank file to a GTF file
- This script was created to show how to quickly convert a raw Genbank file to a GTF file when a GTF file cannot be located. It was created for undergraduate students at The University of Maine.
- Key Skills: perl
- de novo Transcriptome Assembly
- This tutorial walks through using the Trinity de novo transcriptome assembly software on the University of Maine Advanced Computing Group Linux cluster.
- Key Skills: Trinity, Portable Batch System, Linux, Command Line
Project-specific Materials
- Guide to RNA-Seq Analysis with Galaxy: pt.1
- This is a set of instructional materials for aligning RNA-seq reads from the Giles bacteriophage to the genome of its host, Mycobacterium smegmatis. This was done in support of the The University of Maine’s Honors College. The Github repo also contains a link to an RPub page.
- Key Skills: Galaxy
- Guide to RNA-Seq Analysis with Galaxy: pt.2
- This is a continuation of the above project. This is a set of instructional materials for aligning RNA-seq reads from the Giles bacteriophage to its own annotated genome. This was done in support of the The University of Maine’s Honors College. The Github repo also contains a link to an RPub page.
- Key Skills: Galaxy
- Using DESeq2 to Perform Basic Differential Expression Analysis
- This is a set of instructional materials for performing basic differential analysis on RNA-seq reads. It is explicitly designed to be the final module for the work on the Giles bacterioohage above. The Github repo also contains a link to an RPub page.
- Key Skills: R, Bioconductor, DESeq2
- Lobster de novo Transcriptome Assembly
- This tutorial walks through using the Trinity de novo transcriptome assembly software on the University of Maine Advanced Computing Group Linux cluster using a published RNA-Seq dataset from lobster larvae.
- Key Skills: Trinity, Portable Batch System, Linux, Command Line