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Intro
Applications of RNA-Seq data
Schematic detailed workflow
What are splice-aware aligners?
Workflow for this tutorial
Comparison of run times, memory usage and aligner accuracies for various aligners
Which aligner should I choose?
Pre-requistes to build this pipeline (things that will not be covered in this video)
Set-up before building the pipeline
Some good practices while building a pipeline
Quality control: FastQC
To trim or to not trim?
Trimming reads: Trimmomatic
Align reads: HISAT2
Read quantification: featureCounts