1.Module 1 - Introduction to RNA sequencing

1. Installation
2. Reference Genomes
3. Annotations
4. Indexing
5. RNA-seq Data
6. Pre-Alignment QC

2.Module 2 - RNA-seq Alignment and Visualization

1. Adapter Trim
2. Alignment
3. IGV
4. Alignment Visualization
5. Alignment QC

3.Module 3 - Expression and Differential Expression

1. Expression
2. Differential Expression
3. DE Visualization
4. Kallisto for Reference-Free Abundance Estimation

4.Module 4 - Isoform Discovery and Alternative Expression

1. Reference Guided Transcript Assembly
2. de novo Transcript Assembly
3. Transcript Assembly Merge
4. Differential Splicing
5. Splicing Visualization

5.Module 5 - De novo transcript reconstruction

1. De novo RNA-Seq Assembly and Analysis Using Trinity

6.Module 6 - Functional Annotation of Transcripts

1. Functional Annotation of Assembled Transcripts Using Trinotate

4.2 Stringtie De Novo Mode

在上一个模块中，使用Stringtie的'-G'和'-e' 选项在'reference only'模式下运行Stringtie

本次教程将运行Stringle的de novo模式

额外选项如下

• '-p 8' tells Stringtie to use eight CPUs
• '-l' name prefix for output transcripts (default: STRG)
• '-o' output path/file name for the assembled transcripts GTF (default: stdout)

mkdir denovo
stringtie -p 8 -l HBR_Rep1 -o denovo/HBR_Rep1/transcripts.gtf HBR_Rep1.bam
后续处理相同