snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets.
Pipeline | Description |
---|---|
createIndices |
Create indices for an organism for further use within snakePipes |
DNA-mapping |
Basic DNA mapping using bowtie2, filter mapped files, QC and create coverage plots |
ChIP-Seq |
Use the DNA mapping output and run ChIP/Input normalization and peak calling |
ATAC-seq |
Use the DNA mapping output and detect open chromatin regions for ATAC-seq data |
HiC |
Hi-C analysis workflow, from mapping to TAD calling |
noncoding-RNA-Seq |
noncoding-RNA-Seq workflow : From mapping to differential expression of genes and repeat elements using DESeq2 |
mRNA-Seq |
RNA-Seq workflow : From mapping to differential expression using DESeq2 |
scRNA-Seq |
Single-cell RNA-Seq (CEL-Seq2) workflow : From mapping to differential expression |
WGBS |
Whole-genome Bisulfite-Seq analysis workflow, from mapping to DMR calling and differential methylation analysis |
preprocessing |
Merging technical replicates (e.g., across lanes), removing optical duplicates, running FastQC |
- Assuming you have python3 with conda, install snakePipes with:
- You can update snakePipes to the latest version available on conda with:
snakePipes is going to move to mamba in the future.
- Download genome fasta and annotations for an your organism, and build indexes, Check in
createIndices
- Configure snakePipes with paths to organism and cluster configs on your system using snakePipes config. For detailed information, run:
Note
If you have a copy of a shared/defaults.yaml with the necessary paths configured (i.e. from a previous installation), you can pass it to snakePipes config with --oldConfig and --configMode recycle instead of providing all the paths manually again. Config keys have to match for this to work. In the same way, you can pass your external organism yaml folder with --organismsDir
or cluster config with --clusterConfig
.
- Download example fastq files for the human genome here
- Execute the DNA-mapping pipeline using the example command.sh in the test data directory.
For a detail introduction to setting up snakePipes from scratch, please visit content/setting_up
For each organism of interest, snakePipes requires fasta files, genome indexes and annotation files. Paths to these files are specified in the organism/<name>.yaml files. After installation, the location of these files could be revealed by the following command:
You could either modify the existing files (add your own paths), or add a new file there. See more detail in content/running_snakePipes
snakePipes could either be executed locally, or on any snakemake-supported cluster infrastructure. See details for setting up the cluster command in content/running_snakePipes
If you adopt/run snakePipes for your analysis, cite it as follows :
Bhardwaj V, Heyne S, Sikora K, Rabbani L, Rauer M, Kilpert F, Richter AS, Ryan DP, Manke T. snakePipes: facilitating flexible, scalable and integrative epigenomic analysis. Bioinformatics. 2019 May 27. pii: btz436. doi:
10.1093/bioinformatics/btz436. [Epub ahead of print] PubMed PMID: 31134269. https://www.ncbi.nlm.nih.gov/pubmed/31134269
This tool suite is developed by the Bioinformatics Unit at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.
For query/questions regarding snakePipes, please write on biostars with the tag #snakePipes
For feature requests or bug reports, please open an issue on our GitHub Repository.
content/setting_up.rst content/running_snakePipes.rst content/advanced_usage.rst content/workflows/createIndices.rst content/workflows/DNA-mapping.rst content/workflows/ChIP-seq.rst content/workflows/ATAC-seq.rst content/workflows/HiC.rst content/workflows/preprocessing.rst content/workflows/mRNA-seq.rst content/workflows/noncoding-RNA-seq.rst content/workflows/scRNA-seq.rst content/workflows/WGBS.rst content/News.rst
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