转录组丨RNA-seq分析snakemake流程

生信探索 生信分析笔记 2023-06-12 16:19 发表于陕西

A SnakeMake workflow for Bulk RNA-seq

Reads were mapped onto ensembl genome with STAR, and adapters were removed with fastp.

For nomalisztion, gtftools was used to calculate gene_length and bioninfokit was used to give TPM, FPKM and CPM results.

For quality control, PCA plot, dendrogram plot and heatmap were used to show differences among samples or groups.

PyDESeq2 was used to perform differential expression anlysis.

General settings

To configure this workflow, modify config/config.yaml according to your needs, following the explanations provided in the file.

Sample sheet

• Add samples to config/samples.tsv. Only the column Sample is mandatory, but any additional columns can be added.
• For each sample, add one or more sequencing units (runs, lanes or replicates) to the Unit column of config/samples.tsv.
• For each sample, define Group column(experimental or clinical attribute).

Report

QC plot

differential expression anlysis

• MA plot

• volcano plot