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Welcome to the circPipe wiki!

In a nutshell, circPipe (circRNAs Pipeline) aims at data exploration of circRNAs. It begins with raw sequencing data, we recommend our users to use paired-end sequencing data, the sequencing depth should be more than 70M, the read length should be longer than 50bp, and longer than 100bp is the best. We absorb six kinds of common software/work to detect circRNAs, including Circexplorer2, CIRI, Find_circ, Mapsplice, Segemehl and KNIFE. Users can choose one, several or all appropriate software according to their own project. By default, our pipeline will only run CIRI to detect circRNAs. If users chose several kinds of software, our pipeline will combine all results from different software to a sole matrix. To interpret data, we design three modules to explore the identified circRNAs as well as protein coding ones, including conventional annotation, differential circRNA expression analysis and correlation analysis with host genes. Plots and tables of analysis module are presented in a HTML file via Rmarkdown.

The software KNIFE may be a little complicated, the running speed is slow and it will chew up a ton of memory. Our pipeline supports KNIFE,but we will not use it during the test. When users use docker container to run the pipe, it will also not allowed to choose KNIFE. If users still want to use KNIFE, they must download the software that our pipeline provided and configure Paths themselves.

More information can be found in the The cirPipe workflow page, or in the project GitHub wiki. Please be sure that you have all dependencies software or tools preinstalled in you 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 cirPipe in your local server or cluster. This tutorial explain 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.

Workflows

Our Pipeline Steps are showed in the below chart. CircPipe allows you to run arbitrary pipelines among five pipelines. Choose between workflows by using --selectTools 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