ninomoriaty/circpipe repository overview
circPipe
circRNA analysis pipe
Introduction
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 | Pipeline Six |
|---|---|---|---|---|---|---|
| Raw Data QC | Fastp | Fastp | Fastp | Fastp | Fastp | Fastp |
| Reads Alignment | STAR | BWA | Bowtie2 | - | - | - |
| Reads counting | CIRCexplorer2 | CIRI | Find_circ | Mapsplice | Segemehl | KNIFE |
| Data Processing (in house script) | Python,Java,R | Python,Java,R | Python,Java,R | Python,Java,R | Python,Java,R | Python,Java,R |
| Differential expression | edgeR | edgeR | edgeR | edgeR | edgeR | edgeR |
| Summary Report | MultiQC | MultiQC | MultiQC | MultiQC | MultiQC | MultiQC |
Dependencies
- Softwares
- Fastp
- STAR
- CIRCexplorer2
- BWA
- CIRI
- Bowtie2
- Find_circ
- Mapsplice
- Segemehl
- KNIFE
- MultiQC
- Several R packages for downstream analysis.
Tag summary
Content type
Image
Digest
Size
2.3 GB
Last updated
about 7 years ago
docker pull ninomoriaty/circpipe