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Setup RNA-Seq Pipeline From Scratch - Fastq to Counts - Step-by-Step Tutorial
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- 1 Intro
- 2 - Applications of RNA-Seq data
- 3 Schematic detailed workflow
- 4 What are splice-aware aligners?
- 5 Workflow for this tutorial
- 6 Comparison of run times, memory usage and aligner accuracies for various aligners
- 7 Which aligner should I choose?
- 8 Pre-requistes to build this pipeline things that will not be covered in this video
- 9 Set-up before building the pipeline
- 10 Some good practices while building a pipeline
- 11 Quality control: FastQC
- 12 To trim or to not trim?
- 13 Trimming reads: Trimmomatic
- 14 Align reads: HISAT2
- 15 Read quantification: featureCounts
