A Snakemake workflow for wicked-fast paired-end RNA-seq analysis with Salmon and DESeq2.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).
Create a main analysis directory with the subdirectories config/, reads/, and workflow/.
Place all your paired-end fastq files files in the reads folder. These should have the extensions _R1_001.fastq.gz/_R2_001.fastq.gz for read 1 and read2, respectively.
The config/ directory should contain two files: config.yml and samples.csv.
Meta information of the samples are described in samples.csv:
| sample | genotype | treatment | reference | batch |
|---|---|---|---|---|
| Control_1 | WT | Normoxia | yes | 1 |
| Control_2 | WT | Normoxia | yes | 1 |
| Control_Hypoxia_1 | WT | Hypoxia | no | 1 |
| Control_Hypoxia_2 | WT | Hypoxia | no | 1 |
Important
The sample names should correspond to the files name, eg. Control_1_R1_001.fastq.gz and Control_1_R2_001.fastqz for sample Control_1.
Analysis settings and resource
genome: human # human or mouse
gencode_genome_build: 44
fdr_cutoff: 0.05 # adj p value cut off for volcano plots
fc_cutoff: 0.5 # log2 fold change cut off for volcano plots
salmon-quant:
extra_params: "" # additional arguments to pass to Salmon
salmon-index:
extra_params: "--gencode"
deseq2:
# custom model for DESeq2
design: ""
resources: # computing resources
trim:
cpu: 8
time: 60
fastqc:
cpu: 4
time: 60
mapping:
cpu: 8
time: 120
deseq2:
cpu: 6
time: 60
plotting:
cpu: 2
time: 20