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.
To configure this workflow, modify
config/config.yaml according to your needs, following the explanations provided in the file.
- 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
- For each sample, define
Group column(experimental or clinical attribute).
differential expression anlysis