circPipe

circRNA analysis pipe

Introduction

In the recent decades, circular RNA(circRNA) have came into our sight and emerged as a large class of non-coding RNAs. It thought to be predominately generated by covalently back-splicing conjunction of 3’end and 5’end from the same or distinct exons. circRNA involving in a variaty of biological functions in cells. Emerging evidences show that dysregulation of circRNAs are associated with several human diseases including cancer. Therefore, Systematically identification and profiling circRNAs is a fundimental process for dissecting the underlining biological mechanism of its regulation. To date, a range of tools have been developed to investigate circRNAs from high-throughput sequencing including CIRCexplorer2, CIRI, Find_circ, Mapsplice, and Segemehl. However, it not a easy thing for users to pick tools and compare the result from such tools. The most appropriate strategy is run those tools parallel and collapse the result together, and vote the candidates to improve their confidence for further experimental exploration. In addition, a remapping step is nessasary to help reduce the false postive candidates in an application scenarios. Here, we present circPipe, a nextflow-based pipeline for running multitool-based identification of circRNA from RNA-seq dataset. circPipe integrates a remapping stragegy to help filter out the circRNAs with non-reads supported in non-mismatch mode of realignment. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

A full tutorial of CircPipe can be found at Wiki page of this project. plz go to the https://github.com/likelet/circPipe/wiki

Pipeline Steps

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

Dependencies

• Softwares
  • Fastp
  • STAR
  • CIRCexplorer2
  • BWA
  • CIRI
  • Bowtie2
  • Find_circ
  • Mapsplice
  • Segemehl
  • MultiQC
  • Several R packages for downstream analysis.

run analysis with bed format circRNA result

nextflow run /data1/software/circPipe/alternative_mode.nf \
		-c  /data1/software/circPipe/nextflow.config  \
		-with-trace -profile docker,colonCancer \
		-resume --selectTools 1,2,3 --bedDir "place to your bedfiles" \
		--skip_fastp \
		--skipDE \
		--container likelet/circpipe:latest

run QuantCircle analysis with a single bed file

nextflow run /data1/software/circPipe/QuantCircle.nf \
		-with-trace -profile docker \
		--container likelet/circpipe:latest \
		--reads "Fastq/*{1,2}.fq.gz" \
        --bedfile "ciri_pos20190613.candidates.bed"  \
		--genomefile "Genome/hg19_chr2.fa" \
	    --hisat2_index "Genome/hg19_chr2_hisat2_index/hg19_chr2" \