Home

Welcome to the cirPipe wiki!

Pipelines

Pipeline Steps

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

Step	Pipeline One	Pipeline Two	Pipeline Three	Pipeline Four	Pipeline Five
Raw Data QC	Fastp	Fastp	Fastp	Fastp	Fastp
Reads Alignment	STAR	BWA	Bowtie2	-	-
Reads counting	CIRCexplorer2	CIRI	Find_circ	Mapsplice	Segemehl
Data Processing (in house script)	Python,JAVA,R	Python,JAVA,R	Python,JAVA,R	Python,JAVA,R	Python,JAVA,R
Differential expression	edgeR	edgeR	edgeR	edgeR	edgeR
Summary Report	MultiQC	MultiQC	MultiQC	MultiQC	MultiQC