snakeflow

RNA-Seq and ChIP-seq workflow based on snakemake

Dependency

• python 3

  • numpy
  • pandas
  • snakemake
  • matplotlib
  • seaborn
  • gseapy

• hisat2, salmon

• samtools, deeptools, bedtools

• rMATS-turbo, rmats2sashimiplot

• fastqc, rseqc, multiqc

• graphviz

• R

  • DESeq2
  • tximport
  • readr
  • pheatmap
  • ggplot2
  • ggrepel
  • clusterProfiler
  • ChIPSeeker
  • EnsDb.Hsapiens.v86

Installation

Set up running environment. This config file will create a python 3.x env.

bash snakeflow-enviroment-setup.sh

usage

# Step1: activate snakemake
source activate snakeflow

# Step2: clone this repo

# Step3: copy all your fastq files into fastq dir
find . -name "*fastq.gz" | while read id; do cp $id fastq/; done;

# Step4: modify config.yml with your own paramter
# Note: put config.yml in the same dir with your snakefile.
vim  config.yml

# Step5: run snakemake with -np option. this test your ``commands`` runs without any errors.
snakemake -s salmon-tximport-deseq2-v0.2.snakefile -np

# Step6: export workflow charts
snakemake -s salmon-tximport-deseq2-v0.2.snakefile --dag | dot -Tpdf > dag.pdf

# Step7: or using the default snakemake environment you've created above.
snakemake -s salmon-tximport-deseq2-v0.1.snakefile -p -j 8