TOPIC: Transcriptomics

A repository for the lessons and tutorials for the Transcriptomics TOPIC channel of the BVCN

Prerequisites

• A working Unix environment
• Experience with the command line

Overview

This BVCN topic will cover:

• An overview of transcriptomics and metatranscriptomics
• Lessons covering various applications, including:
  • Wetlab and in silico rRNA depletion
  • Recovery/removal of rRNA from metatranscriptomic data

Lesson 1

Title: Introduction to Transcriptomics

Instructors: Arkadiy Garber

• What is a transcriptome?
• Case studies using transcriptomics:
  • Differential gene expression
  • Gene expression by community (metatranscriptomics)
  • Combining metatranscriptomics and metagenomics
• General transcriptomic pipeline overview
• Transcript assemblers and read aligners

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Lesson 2

Title: rRNA depletion (wet lab and in silico)

Instructors: Arkadiy Garber

• Why remove rRNA from you RNA samples?
• Various wet-lab rRNA depletion methods:
  • NEBNext rRNA depletion using RNase H
  • NEBNext mRNA enrichment using magnetic beads
  • DIY method using probes and streptavidin-coated magnetic beads
  • DASH: using Cas9 to remove unwatned high-abundance sequences
  • Illumina RiboZero kits
• Brief SortMeRNA intro

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Watch the tutorial

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Lesson 3

Title: Read counting with htseq-count

Instructors: Arkadiy Garber

• Generating count tables: where this is in the RNA seq pipeline
• The HTSeq framework
• htseq-count
• read mapping paramaters
• count table output
• comparison to other read counting tools

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Watch the tutorial

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Lesson 4

Title: RNA assembly with Trinity

Instructors: Alexis Marshall

• Read QC and assessment prior to assembly
• rRNA depletion
• Trinity

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