RNA-seq

TODO Summary

How to analyze RNA-seq data

Understand what the data looks like

1. Quality control

• Larger error means the data quality is poor

• Identify failed sequencing experiments

• Filter out those low quality reads

• Trim off those low quality fragments

• Reduce sequencing error caused noise as much as possible for downstream analysis

2. Mapping to reference database

3. Quantify gene expression

4. Identify differentially expressed genes

TSS Assays

• GRO-cap

• PRO-cap

• CoPRO

• Start-seq

• CAGE

• RAMPAGE

• NET-CAGE

• csRNA-seq

• STRIPE-seq

Nascent Transcript Assays

• GRO-seq

• PRO-seq

• mNET-seq

• Bru-seq

• BruUV-seq