A RNAseq pipeline from raw reads to feature counts
This is is the rnaseq pipeline from the Sequana projet
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_rnaseq
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.
This pipelines requires the following executable(s):
- featureCounts (subread package)
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.
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.
the RNAseQC rule is switch off and is not currently functional in version 0.9.X
|0.9.3||if a fastq_screen.conf is provided, we switch the fastqc_screen section ON automatically|
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