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Welcome to the RNAseqPipe wiki!

RNAseqPipe (RNAseq Pipeline) aims at data exploration of RNAseq data set. It begins with the raw sequencing data and then following a step of quality control. We recommend our users to use the Illumina generated paired-end/singled-end sequences and the sequencing depth should be more than 10M. The length of the reads should be longer than 50bp

More information can be found in The RNAseqPipe workflow page, or in the project GitHub wiki. Please be sure that you have all dependencies software or tools preinstalled in your system. Otherwise, we recommended that users employ docker or singularity containers to run the pipe.

This wiki includes several tutorials, plz following the step by step tutorial to run RNAseqPipe in your local server or cluster. This tutorial explains how to set the parameters in the nextflow.config file, and describe the files that will be produced in output, while at this page you can know more about How to read the logs.

Pipeline Steps

The pipeline allows you to choose between running either replicate or without replicates. Choose between workflows by using --without_replicate or not(default).

Step	With replicates	without_replicate
Raw data QC	Fastp	Fastp
Align Reads	STAR	STAR
Alignment QC	Qualimap	Qualimap
Reads counting	RSEM	RSEM
Matrix collapses	DAtools	DAtools
Differential expression	DESeq2	Poisson Test(DAtools)
Gene Set enrichment Analysis	GSEA	-
Summary Report	MultiQC	MultiQC