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This is a personal project focused on creating uniformal pipeline for processing RNA-seq data with the end goal to create a .Rdata object which can be imported into R/Shiny app for downstream analysis and hypothesis testing.

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ajandria/futuriandge

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Nextflow run with conda run with docker run with singularity

Introduction

Welcome to DE_RNA-Seq_nf - a bioinformatics best-practice analysis pipeline for up-stream processing of RNA-Seq data with the main focus on differential expression analysis.

Run test data as:

nextflow run ajandria/futuriandge -r main -latest -profile cluster,conda,test --organism mouse --outDir .

Standard pipeline run:

nextflow run ajandria/futuriandge -r main -latest -profile cluster,singularity --organism mouse/human --outDir . --input samplesheet.csv

Currently the pipeline supports only the MUB infrastructure (hardcoded references).

About

This is a personal project focused on creating uniformal pipeline for processing RNA-seq data with the end goal to create a .Rdata object which can be imported into R/Shiny app for downstream analysis and hypothesis testing.

Topics

rna-seq pipeline nextflow differential-expression nextflow-dsl2

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BSD-4-Clause license

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