snakePipes ========== .. image:: content/images/snakePipes_small.png :scale: 20 % :height: 200px :width: 200 px snakePipes are pipelines built using `snakemake `__ and *python* for the analysis of epigenomic datasets. Below is the list of pipelines available in snakePipes ------------------------------------------------------ =============================== =============================================================================================================== Pipeline Description =============================== =============================================================================================================== :ref:`createIndices` Create indices for an organism for further use within snakePipes :ref:`DNA-mapping` Basic DNA mapping using bowtie2, filter mapped files, QC and create coverage plots :ref:`ChIP-Seq` Use the DNA mapping output and run ChIP/Input normalization and peak calling :ref:`ATAC-seq` Use the DNA mapping output and detect open chromatin regions for ATAC-seq data :ref:`HiC` Hi-C analysis workflow, from mapping to TAD calling :ref:`noncoding-RNA-Seq` noncoding-RNA-Seq workflow : From mapping to differential expression of genes and repeat elements using DESeq2 :ref:`mRNA-Seq` RNA-Seq workflow : From mapping to differential expression using DESeq2 :ref:`scRNA-Seq` Single-cell RNA-Seq (CEL-Seq2) workflow : From mapping to differential expression :ref:`WGBS` Whole-genome Bisulfite-Seq analysis workflow, from mapping to DMR calling and differential methylation analysis :ref:`preprocessing` Merging technical replicates (e.g., across lanes), removing optical duplicates, running FastQC =============================== =============================================================================================================== Quick start ----------- * Assuming you have *python3* with *conda*, install the latest version of snakePipes with: .. code:: bash conda install mamba -c conda-forge && mamba create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes * You can update snakePipes to the latest version available on conda with: .. code:: bash mamba update -n snakePipes -c mpi-ie -c conda-forge -c bioconda --prune snakePipes snakePipes is going to move to mamba in the future. * Download genome fasta and annotations for an your organism, and build indexes, Check in :ref:`createIndices` * Configure snakePipes with paths to organism and cluster configs on your system using snakePipes config. For detailed information, run: .. code:: bash snakePipes config --help .. 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. Running your own analysis ------------------------- For a detail introduction to setting up snakePipes from scratch, please visit :doc:`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/.yaml files. After installation, the location of these files could be revealed by the following command: .. code:: bash snakePipes info You could either modify the existing files (add your own paths), or add a new file there. See more detail in :doc:`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 :doc:`content/running_snakePipes` Citation ------------- 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 .. image:: content/images/logo_mpi-ie.jpg This tool suite is developed by the `Bioinformatics Unit `_ at the `Max Planck Institute for Immunobiology and Epigenetics `_, Freiburg. Help and Support ---------------- 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 `__. Contents: --------- .. toctree:: :maxdepth: 2 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 Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`