Metadata-Version: 1.2
Name: sequana-rnaseq
Version: 0.14.0
Summary: A RNAseq pipeline from raw reads to feature counts
Home-page: https://github.com/sequana/
Author: thomas cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: thomas cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Description: 
        
        .. image:: https://badge.fury.io/py/sequana-rnaseq.svg
             :target: https://pypi.python.org/pypi/sequana_rnaseq
        
        .. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
            :target: http://joss.theoj.org/papers/10.21105/joss.00352
            :alt: JOSS (journal of open source software) DOI
        
        .. image:: https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg
           :target: https://github.com/sequana/rnaseq/actions/workflows    
        
        
        
        This is is the **rnaseq** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
        
        :Overview: RNASeq analysis from raw data to feature counts
        :Input: A set of Fastq Files and genome reference and annotation.
        :Output: MultiQC reports and feature Counts
        :Status: Production
        :Citation(sequana): Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
        :Citation(pipeline): 
            .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4047837.svg
               :target: https://doi.org/10.5281/zenodo.4047837
        
        Installation
        ~~~~~~~~~~~~
        
        You must install Sequana first::
        
            pip install sequana
        
        Then, just install this package::
        
            pip install sequana_rnaseq
        
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_rnaseq --help
            sequana_pipelines_rnaseq --input-directory DATAPATH --genome-directory genome --aligner star
        
        This creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline::
        
            cd rnaseq
            sh rnaseq.sh  # for a local run
        
        This launch a snakemake pipeline. If you are familiar with snakemake, you can 
        retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::
        
            snakemake -s rnaseq.rules -c config.yaml --cores 4 --stats stats.txt
        
        Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
        
        Requirements
        ~~~~~~~~~~~~
        
        This pipelines requires lots of third-party executable(s). Here is a list that
        may change. A Message will inform you would you be missing an executable:
        
        - bowtie
        - bowtie2
        - STAR
        - featureCounts (subread package)
        - picard
        - multiqc
        
        You can install most of the tools using `damona <https://damona.readthedocs.io>`_::
        
            damona create --name sequana_tools
            damona activate sequana_tools
            damona install sequana_tools
        
        Or use the conda.yaml file available in this repository. If you start a new
        environment from scratch, those commands will create the environment and install
        all dependencies for you::
        
            conda create --name sequana_env python 3.7.3 
            conda activate sequana_env
            conda install -c anaconda qt pyqt>5
            pip install sequana
            pip install sequana_rnaseq
            conda install --file https://raw.githubusercontent.com/sequana/rnaseq/master/conda.yaml
        
        
        .. image:: https://raw.githubusercontent.com/sequana/sequana_rnaseq/master/sequana_pipelines/rnaseq/dag.png
        
        
        Details
        ~~~~~~~~~
        
        This pipeline runs a **RNA-seq** analysis of sequencing data. It runs in 
        parallel on a set of input FastQ files (paired or not). 
        A brief HTML report is produced together with a MultiQC report.
        
        This pipeline is complex and requires some expertise for the interpretation.
        Many online-resources are available and should help you deciphering the output. 
        
        Yet, it should be quite straigtforward to execute it as shown above. The
        pipeline uses bowtie1 to look for ribosomal contamination (rRNA). Then, 
        it cleans  the data with cutapdat if you say so (your data may already be
        pre-processed). If no adapters are provided (default), reads are 
        trimmed for low quality bases only. Then, mapping is performed with standard mappers such as 
        star or bowtie2 (--aligner option). Finally,
        feature counts are extracted from the previously generated BAM files. We guess
        the strand and save the feature counts into the directoy
        ./rnadiff/feature_counts. 
        
        The pipelines stops there. However, RNA-seq analysis are followed by a different
        analysis (DGE hereafter). Although the DGE is not part of the pipeline, you can
        performed it with standard tools using the data in ./rnadiff directory. One such
        tool is provided within our framework (based on the well known DEseq2 software).
        
        Using our framework::
        
            cd rnadiff
            sequana rnadiff --design design.csv --features all_features.out --annotation ANNOT \
                   --feature-name FEAT --attribute-name ATTR
        
        where ANNOT is the annotation file of your analysis, FEAT and ATTR the attribute
        and feature used in your analysis (coming from the annotation file).
        
        This produces a HTML repot summarizing you differential analysis.
        
        
        Rules and configuration details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_rnaseq/master/sequana_pipelines/rnaseq/config.yaml>`_
        to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 
        
        
        .. warning:: the RNAseQC rule is switch off and is not currently functional in
           version 0.9.X
        
        Changelog
        ~~~~~~~~~
        
        ========= ====================================================================
        Version   Description
        ========= ====================================================================
        0.14.0    * Allow the aligners to have dedicated index for each version in the
                    same genome directory.
                  * Ribosomal is now estimated on the first 100,000 reads to speed up
                    analysis
                  * --indexing and --force-indexing  options not required anymore. 
                    Indexing will be done automatically and not redone if present.
                  * Use of the new sequana-wrappers repository
        0.13.0    * Major update to use the new sequana version and the RNADiff tools.
                  * remove fastq_screen. One can use sequana_multitax for taxonomic
                    content and contamination.
                  * cutadapt is now replaced by fastp, although it can still be used.
                  * full integration of salmon for prokaryotes and eukaryotes
                  * user interface has now a --skip-gff-check option. Better handling of
                    input gff with more meaningful messages
                  * integration of rseqc tool
        0.12.1    * indexing was always set to True in the config after 0.9.16 update. 
        0.12.0    * BUG fix: Switch mark_duplicates correctly beore feature counts
        0.11.0    * rnadiff one factor is simplified
                  * When initiating the pipeline, provide information about the GFF
                  * mark duplicates off by default
                  * feature_counts has more options in the help. split options into
                    feature/attribute/extra_attributes.
                  * HTML reports better strand picture and information about rRNA
                  * refactorising the main standalone and config file to split feature
                    counts optiions into feature and attribute. Sanoty checks are ow
                    provided (--feature-counts-attribute, --feature-counts-feature-type)
                  * can provide a custom GFF not in the genome directory
                  * can provide several feature from the GFF. Then, a custom GFF is
                    created and used
                  * fix the --do-igvtools and --do-bam-coverage with better doc
        0.10.0    * 9/12/2020
                  * Fixed bug in sequana/star_indexing for small genomes (v0.9.7). 
                    Changed the rnaseq requirements to benefit from this bug-fix that
                    could lead to seg fault with star aligner for small genomes.
                  * Report improved with strand guess and plot
        0.9.20    * 7/12/2020
                  * BUG in sequana/star rules v0.9.6. Fixed in this release.
                  * In config file, bowtie section 'do' option is removed. This is now
                    set automatically if rRNA_feature or rRNA_file is provided. This
                    allows us to skip the rRNA mapping entirely if needed.
                  * fastq_screen should be functional. Default behaviour is off. If 
                    set only phiX174 will be search for. Users should build their own
                    configuration file.
                  * star/bowtie1/bowtie2 have now their own sub-directories in the 
                    genome directory. 
                  * added --run option to start pipeline automatically (if you know
                    what you are doing)
                  * rnadiff option has now a default value (one_factor)
                  * add strandness plot in the HTML summary page
        0.9.19    * Remove the try/except around tolerance (guess of strandness) to 
                    make sure this is provided by the user. Final onsuccess benefits
                    from faster GFF function (sequana 0.9.4)
        0.9.18    * Fix typo (regression bug) + add tolerance in schema + generic 
                    title in multiqc_config. (oct 2020)
        0.9.17    * add the *tolerance* parameter in the feature_counts rule as a user
                    parameter (config and pipeline). 
        0.9.16    * Best feature_counts is now saved into rnadiff/feature_counts 
                    directory and rnadiff scripts have been updated accordingly
                  * the most probable feature count option is now computed more
                    effectivily and incorporated inside the Snakemake pipeline (not in
                    the onsuccess) so that multiqc picks the best one (not the 3 
                    results)
                  * the target.txt file can be generated inside the pipeline if user
                    fill the rnadiff/conditions section in the config file
                  * indexing options are filled automatically when calling
                    sequana_rnaseq based on the presence/absence of the index 
                    of the aligner being used.
                  * salmon now integrated and feature counts created (still WIP in
                    sequana)
        0.9.15    * FastQC on raw data skipped by default (FastQC
                    for processed data is still available)
                  * Added paired options (-p) for featureCounts
                  * Switch back markduplicates to False for now.
        0.9.14    * Use only R1 with bowtie1
                  * set the memory requirements for mark_duplicates in cluster_config
                    file
                  * Set temporary directory for mark_duplicates to be local ./tmp
        0.9.13    * set mark_duplicate to true by default
                  * use new sequana pipeline manager
                  * export all features counts in a single file
                  * custom HTML report
                  * faster --help calls
                  * --from-project option added
        0.9.12    * include salmon tool as an alternative to star/bowtie2
                  * include rnadiff directory with required input for Differential
                    analysis
        0.9.11    * Automatic guessing of the strandness of the experiment
        0.9.10    * Fix multiqc for RNAseQC rule
        0.9.9     * Fix RNAseQC rule, which is now available. 
                  * Fix ability to use existing rRNA file as input
        0.9.8     * Fix indexing for bowtie1 to not be done if aligner is different
                  * add new options: --feature-counts-options and --do-rnaseq-qc,
                    --rRNA-feature
                  * Based on the input GFF, we now check the validity of the rRNA
                    feature and feature counts options to check whether the feature 
                    exists in the GFF
                  * schema is now used to check the config file values
                  * add a data test for testing and documentation
        0.9.7     * fix typo found in version 0.9.6
        0.9.6     * Fixed empty read tag in the configuration file
                  * Possiblity to switch off cutadapt section
                  * Fixing bowtie2 rule in sequana and update the pipeline accordingly
                  * Include a schema file
                  * output-directory parameter renamed into output_directory (multiqc 
                    section)
                  * handle stdout correctly in fastqc, bowtie1, bowtie2 rules
        0.9.5     * Fixed https://github.com/sequana/sequana/issues/571
                  * More cutadapt commands and sanity checks
                  * Fixed bowtie2 options import in rnaseq.rules
        0.9.4  
        0.9.3     if a fastq_screen.conf is provided, we switch the fastqc_screen 
                  section ON automatically
        0.9.0     **Major refactorisation.**
        
                  * remove sartools, kraken rules. 
                  * Indexing is now optional and can be set in the configuration.
                  * Configuration file is simplified  with a general section to enter
                    the genome location and aligner. 
                  * Fixed rules in  sequana (0.8.0) that were not up-to-date with
                    several executables used in the  pipeline including picard,
                    fastq_screen, etc. See Sequana Changelog for details with respect
                    to rules changes. 
                  * Copying the feature counts in main directory  ready to use for 
                    a differential analysis.
        ========= ====================================================================
        
Keywords: snakemake, sequana, RNAseq, RNADiff, differential analysis
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
