sequana-rnaseq 0.9.8

A RNAseq pipeline from raw reads to feature counts

This is is the rnaseq pipeline from the Sequana projet

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:

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

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 interface.

Requirements

This pipelines requires the following executable(s):

• bowtie

• bowtie2

• STAR

• featureCounts

• picard

• multiqc

More may be needed depending on the configuration file options. For instance, you may use fastq_screen, in which case you need to install it and configure it.

Details

This pipeline runs rnaseq in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced.

Rules and configuration details

Here is the latest documented configuration file 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
0.9.8	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.