Writen by Kristen Wells
A collection of snakemake pipelines to analyze omics datasets. Current pipelines include:
- A scRNA-sequencing pipeline that analyzed 10x genomics datasets. Can be used with scRNA-seq, scCITE-seq, scVDJ-seq, and hashtagging (and any combination of those).
- A basic bulk RNA-sequencing pipeline that includes options for trimming (cutadapt, bbduk or none). The pipeline includes alignment with star and read counting with FeatureCounts. This pipeline will output a quality Rmarkdown as the final step.
- A pipeline to process ChIP-seq data that includes options for trimming (cutadapt, bbduk, or none). The pipeline includes alignment iwth bowtie2, peak calling with Macs2 and initial analysis with diffbind. This pipeline will output a quality Rmarkdown as the final step.
Pipelines that will be added soon include:
- An ATAC-seq pipeline
Snakemake pipelines here were written to work on a slurm cluster but should be easily ported to other systems. All pipelines rely on docker and singularity images.
Snakemake must be installed to use these pipelines.
- Download and install miniconda3: For Linux
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh
- Install Snakemake:
conda install snakemake -c bioconda -c conda-forge
Steps to run indivdual pipelines are within their own directories.
If you use any of the pipelines in this repository, please give appropriate credit.