Introduction

Welcome to the cirPipe Wiki! This is a pipeline for data exploration of circRNAs.

Our pipeline begins with raw sequencing reads in fastq format. Users can provide reference index files as an input for the pipeline, and Hg19 is the default.

Our pipeline will proceed a step of quality control for the input raw reads firstly, then the decontaminated reads and reference index files will be used as input files for the next step.

Our pipeline absorb six kinds of built-in software to detect circRNAs in total, including circexploere2, Find_circ, Mapsplice, CIRI, Segemehl and KNIFE. Users can choose one, several or all software as their own will. If users didn’t make a choice at the beginning, the pipeline will use CIRI to detect circRNAs by default. If users chose several kinds of software, our pipeline will then combine all these results in to a sole matrix.

Our pipeline will also use the final matrix file for the following analysis, including annotation, differential gene expression analysis and correlation analysis. All results of these analysis will be presented as tables and plots in the final report.

In the end, our pipeline will provide a final report to the users. For more details in the pipeline usages, please go on reading other parts of the circPipe Wiki.

Welcome to use our pipeline!