1.Module 1 - Introduction to RNA sequencing
- Installation
- Reference Genomes
- Annotations
- Indexing
- RNA-seq Data
- Pre-Alignment QC
2.Module 2 - RNA-seq Alignment and Visualization
- Adapter Trim
- Alignment
- IGV
- Alignment Visualization
- Alignment QC
3.Module 3 - Expression and Differential Expression
- Expression
- Differential Expression
- DE Visualization
- Kallisto for Reference-Free Abundance Estimation
4.Module 4 - Isoform Discovery and Alternative Expression
- Reference Guided Transcript Assembly
- de novo Transcript Assembly
- Transcript Assembly Merge
- Differential Splicing
- Splicing Visualization
5.Module 5 - De novo transcript reconstruction
- De novo RNA-Seq Assembly and Analysis Using Trinity
6.Module 6 - Functional Annotation of Transcripts
- Functional Annotation of Assembled Transcripts Using Trinotate
4.2 Stringtie De Novo Mode
在上一個(gè)模塊中，使用Stringtie的'-G'和'-e' 選項(xiàng)在'reference only'模式下運(yùn)行Stringtie
本次教程將運(yùn)行Stringle的de novo模式
額外選項(xiàng)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
后續(xù)處理相同
