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License: MIT License

R 3.11% Shell 4.64% Python 39.83% Makefile 8.65% Perl 34.44% Roff 9.31% Perl 6 0.01% Batchfile 0.01%

srna_analysis_maize's Introduction

small RNA-seq data analysis in maize

This repository is being developed for providing an entire workflow for processing small RNA sequencing data in maize. This directory includes key scripts for analyzing miRNAs, isomiRs, phasiRNAs, mutant and degradome data.

How to start:

Set up the dependency environment based on conda

    ## Creating an environment
    conda env create -f environment.yml

    ## Exporting an environment
    conda env export > environment.yml

Run the pipeline based on snakemake

    ## Drawing the scheme
    snakemake --snakefile sRNA_workflow.smk -np --dag | dot -Tpdf > sRNA_workflow.pdf

    ## Running the pipeline
    snakemake --snakefile sRNA_workflow.smk --cores 20 --latency-wait 120

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