README.md

module4_RNAseq

The fourth module of the 2018 Bioinformatics Community of Practice at BecA-ILRI Hub

Overview of RNA-seq

We will present an overview of how the RNA-Seq samples are produced and the drawbacks of aligning the reads naively to a genomic reference

In the exercises we will explore the test dataset.

Mapping reads to a known transcriptome

We will use a mini test set to align the reads to a) the transcriptome (kallisto) and b) The reference with the annotation.

SNP calling and VCF files

We will use the BAM files from b) to call for SNPs with freebayes (or samtools directly?)

Differential expression

We will explore different R packages for Differential expression (please state the ones you are planning to use).

Transcriptome assembly

We will use the same reads to make a de-novo assembly and produce a putative functional annotation (trinity and cufflinks)

Gene Ontology.

We will use TRAPID to annotate some genes.