simulate-rnaseq
Simple workflow to simulate RNA-seq reads and perform DE-analysis.
Workflow simulates RNA-seq reads using Polyester R package https://github.com/alyssafrazee/polyester, quantifies expression with Salmon https://combine-lab.github.io/salmon/ and performs DE-analysis using DESeq2 R package https://bioconductor.org/packages/release/bioc/html/DESeq2.html.
Human protein coding transcript sequences are downloaded from https://www.gencodegenes.org/human/. Transcript sequences can be customised by directly editing Snakefile.
Install
To install clone this repository and install dependencies (assumes that conda/miniconda is already installed):
conda env create -f environment.yml
This command creates conda environment called "simulaternaseq".
Running
Activate conda environment:
conda activate simulaternaseq
For test run replace "-j" flag with "-n":
snakemake -j --use-conda
To generate snakemake run report:
snakemake --report output/report.html
Some outputs of interest
File output/diffexp/group1-vs-group2.diffexp.tsv
contains differential expression results, which can be compared to ground truth in output/simulated_reads/sim_tx_info.txt
.
Acknowledgements
The workflow borrowed bits and pieces from rna-seq-star-deseq2 https://github.com/snakemake-workflows/rna-seq-star-deseq2.