Brief introduction to Linux
Linux OS. Using the terminal, commands and utilities to operate on files and directories. Examples to operate on fasta and fastq files.
Quality control and pre-processing of fastq files
Fastq format. FastQC package and fastx_toolkit for pre-processing fastq files.
SAM format and samtools
Overview of bioinformatic pipelines for RNA sequencing data. Samtools package to operate and extract information from sam files.
Overview and step-by-step pipeline. Description of input files and ribosomal RNA filtering. Mapping to reference genome. Transcript assembly and quantification. Differential expression analysis and downstream analysis.
Small RNA sequencing
Special considerations for small RNA sequencing. Mapping to reference genome. Classification according to size. Example of a pipeline for differential expression analysis. Tools for miRNA target prediction.
Characteristics of long non-coding RNA (lncRNA). Step-by-step pipeline for lncRNA discovery.