The small RNA-Seq description pipeline is a Snakemake pipeline to annotate small RNA loci (miRNAs, phased siRNAs) using one or more reference genomes and based on experimental small RNA-Seq datasets.
This pipeline heavily relies on the ShortStack software that annotates and quantifies small RNAs using a reference genome.
Upon completion, several outputs will be generated for each sample:
Results.txt. See the description of this file in the Shortstack manual.These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
This Snakemake pipeline make use of the conda package manager to install softwares and dependencies.
conda, create a virtual environment called snakemake to install Snakemake (version 5.4.3 or higher) by executing the following code in a Shell window: conda env create -f environment.yml. This will install snakemake version 5.20.0 and pandas version 0.25.0 in a new environment called small.conda activate smallIf you have set up conda and created the small environment, that's all you need to do!
A series of custom Python functions are also used and can be found in the helpers.py file.
Versions of softwares and packages can be seen in their respective environment .YAML file in the envs/ folder.
A small dataset is available in test/ to run some tests rapidly. It will use the genome and miRBase reference fasta files stored in refs/.
To run the test, open a new Shell window and:
conda activate smallsnakemake -j 1 -np for a dry run. No analysis is run but it checks that the Directed Acyclic Graph of jobs is OK (input and output from each rule chained to each other).snakemake --cores N where N is the number of CPUs that you want to use (default = 1).A samples.tsv file can be used to specify sample names, their corresponding genomic reference to use and the location of their sequencing file.
Configuration settings can be changed in the config.yaml file. For instance, one could modify the minimal coverage required by Shorstack to discover sRNA loci.
Different genomic references can be used for each sample. Simply provide a genomic reference corresponding to your sample.
...as soon as we have published this software!
This project is licensed under the MIT License - see the LICENSE.md file for details
SemVer is used for versioning. For the versions available, see the releases on this repository.
Content type
Image
Digest
Size
151.9 MB
Last updated
almost 6 years ago
docker pull bleekerlab/small-rna-seq