Guide to RNA-seq Analysis

Introduction
Preparations
Raw read processing
- QC & trimming
- Mapping & quantification
  - Alignment-free method
  - Alignment-based method
Differential expression analysis in R

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Environment
Directories

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Work environment

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Last updated 4 years ago

Environment

CPU: Intel® Xeon® E5-2623 v3 (Quad-Core; 8 Threads)
Memory: 64 GB
Ubuntu 18.04.4 LTS
R version 3.6.2 (2019-12-12)

CPU usage is limited to 6 threads and memory to 32 GB where applicable

Directories

Path

Purpose

/home/USER/tools

Software/tools

/home/USER/db/refanno

Reference genome, annotation and index

/home/USER/SSAPs

RNA-seq exercise on sessile serrated adenomas/polyps dataset

/home/USER/SSAPs/fastqs

FASTQ files

/home/USER/SSAPs/trimmed

Trimmed FASTQ files

/home/USER/SSAPs/salmon

Output from Salmon

/home/USER/SSAPs/star

Output from STAR

/home/USER/SSAPs/salmon_star

Output from STAR+Salmon

/home/USER/SSAPs/rsem_star

Output from STAR+RSEM

/home/USER/SSAPs/analysis

R analysis (DGE, DTE, and DTU)