TOPIC: Transcriptomics
- A working Unix environment (though practice environments are available for lessons below)
- Experience with the command line
- Lesson 1: Introduction to Transcriptomics
- Lesson 2: rRNA depletion methods
- Lesson 3: Read Counting with htseq-count
- Lesson 4: RNA assembly with Trinity
Date posted: 22 April 2020
Author(s): Arkadiy Garber
Instructor(s): 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
Date posted: 27 April 2020
Author(s): Arkadiy Garber
Instructor(s): 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
Date posted: 27 April 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
Date posted: 15 June 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- Generating count tables: where this is in the RNA seq pipeline
- The HTSeq framework
- comparison to other read counting tools
Date posted: 15 Juen 2020
Author(s): Arkadiy Garber
Instructor(s): Arkadiy Garber
- htseq-count
- read mapping paramaters
- count table output
Content | Video presentation |
Primary tools/programs used:
Date posted: 2 Auguest 2020
Author(s): Arkadiy Garber Dr. Alexis Marshall, Dr. Ella Sieradzki
Instructor(s): Dr. Alexis Marshall
- Read QC and assessment prior to assembly
- rRNA depletion
- Trinity
Content | Video presentation |
Primary tools/programs used: