.. _`rna-count-salmon (⤫ legacy)`: RNA-COUNT-SALMON (⤫ LEGACY) =========================== Version: 11-07-2019 Tags: RNA-Seq / Count / Salmon / Abundance Estimation Salmon uses the pseudo mapping approach to estimate the k-mers abundance within your RNA-Seq reads. You may find more information about Salmon at: * https://salmon.readthedocs.io/en/latest/index.html * https://github.com/tdayris-perso/rna-count-salmon.git .. role:: bash(code) :language: bash Pipeline dependencies --------------------- This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically. Conda: * conda-forge::python=3.8.2 * conda-forge::pytest=5.4.2 * conda-forge::datrie=0.8.2 * conda-forge::git=2.26.2 * conda-forge::jinja2=2.11.2 * conda-forge::pygraphviz=1.5 * conda-forge::flask=1.1.2 * conda-forge::pandas=1.0.3 * conda-forge::zlib=1.2.11 * conda-forge::openssl=1.1.1g * conda-forge::networkx=2.4 * bioconda::snakemake=5.19.3 * conda-forge::singularity=3.5.3 Additionally, the following prerequisites are non-optional: * Conda * Genome sequence and annotation Input files ----------- Please find below the list of required input files: * Fastq-formatted **transcriptome** sequences * GTF-formatted **genome** annotation Output files ------------ Please find below the list of expected output files: * TSV formatted abundance estimation * Optional FastQC and MultiQC reports * Complete quantification report embedding material and methods Notes ----- This pipeline takes the cold storage into account. No need to copy your data in advance. In order to install, use "conda" to install required environment, and "git" to clone the git repository. Installation ------------ While installing the workflow, you may run the following commands (order matters): .. list-table:: :widths: 10 80 :header-rows: 1 :align: left * - Case - Command line * - git - .. code-block:: bash # This command clones the github repository if [ ! -d "${RNA_COUNT_SALMON_DIR:?}" ]; then git clone https://github.com/tdayris-perso/rna-count-salmon.git "${RNA_COUNT_SALMON_DIR:?}"; fi * - conda - .. code-block:: bash # This command creates the conda virtual environment. It requires an # access to the git repository (see above). conda env create --force --file "${STRONGR_DIR:?}/workflows/genomic-expression/rna-count-salmon/environment.yaml" Testing ------- In order to test the pipeline, you may try the following commands: .. list-table:: :widths: 10 80 :header-rows: 1 :align: left * - Case - Command line * - quick-test - .. code-block:: bash cd "${RNA_COUNT_SALMON_DIR:?}" make conda tests make all-unit-tests make test-conda-report.html make clean Preparation ----------- In order to prepare a run, you may try the following commands: .. list-table:: :widths: 10 80 :header-rows: 1 :align: left * - Case - Command line * - activate - .. code-block:: bash # This command activates the conda environment available after the # installation process. conda activate rna-count-salmon || source activate rna-count-salmon * - gustaveroussy-references-hg38 - .. code-block:: bash # This points to HG38 references for Gustave Roussy's flamingo FASTA="/mnt/beegfs/database/bioinfo/Index_DB/Fasta/Gencode/GRCH38/RNA/gencodeV27_transcripts.fa" GTF="/mnt/beegfs/database/bioinfo/Index_DB/GTF/Gencode/GRCH38/gencodeV27.gtf" COLD_STORAGE=(/mnt/isilon /mnt/archivage) * - config - .. code-block:: bash # This command builds the configuration file python3.8 "${RNA_COUNT_SALMON_DIR:?}/scripts/prepare_config.py" "${FASTA:?}" "${GTF:?}"--cold_storage "${COLD_STORAGE:?}" --workdir "${RNA_COUNT_SALMON_PREPARE_DIR:?}" --aggregate --libType A * - paired-end-design - .. code-block:: bash #This command builds the design file for pair-ended data python3.7 "${RNA_COUNT_SALMON_DIR:?}/scripts/prepare_design.py" "${RNA_COUNT_SALMON_PREPARE_DIR:?}" * - single-end-design - .. code-block:: bash # This command builds the design file for single-ended data python3.7 "${RNA_COUNT_SALMON_DIR:?}/scripts/prepare_design.py" "${RNA_COUNT_SALMON_PREPARE_DIR:?}" --single Execution --------- In order to execute the pipeline, you may run the following commands: .. list-table:: :widths: 10 80 :header-rows: 1 :align: left * - Case - Command line(s) * - local - .. code-block:: bash source activate rna-count-salmon || conda activate rna-count-salmon snakemake -s "${RNA_COUNT_SALMON_DIR:?}/Snakefile" -r -p --configfile config.yaml -j 4 --use-conda * - torque - .. code-block:: bash # While reserving optimal threads and memory requirements, # the choice of the queue might not be optimal. # See profiles below. source activate rna-count-salmon || conda activate rna-count-salmon snakemake -s "${RNA_COUNT_SALMON_DIR:?}/Snakefile" -r -p --configfile config.yaml -j 100 --cluster "qsub -V -d ${RNA_COUNT_SALMON_WORKDIR:?} -j oe -l nodes=1:ppn={threads},mem={resources.mem_mb}mb,walltime={resources.time_min}:00" --use-conda * - slurm - .. code-block:: bash # While reserving optimal threads and memory requirements, # the choice of the queue might not be optimal. # See profiles below. source activate rna-count-salmon || conda activate rna-count-salmon snakemake -s "${RNA_COUNT_SALMON_DIR:?}/Snakefile" -r -p --configfile config.yaml -j 100 --cluster "sbatch --mem={resources.mem_mb} --time={resources.time_min} --cpus-per-task={threads}" --use-conda * - profile - .. code-block:: bash {'\# Requires slurm profile installation, see': None} source activate rna-count-salmon || conda activate rna-count-salmon snakemake -s "${RNA_COUNT_SALMON_DIR:?}/Snakefile" --configfile config.yaml --profile slurm * - report - .. code-block:: bash snakemake -s "${RNA_COUNT_SALMON_DIR:?}/Snakefile" --configfile config.yaml --report