https://github.com/datngu/circall_quant
Circall_quant: fast circRNA quantification with Quasi-mapping
https://github.com/datngu/circall_quant
Last synced: 2 months ago
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Circall_quant: fast circRNA quantification with Quasi-mapping
- Host: GitHub
- URL: https://github.com/datngu/circall_quant
- Owner: datngu
- Created: 2023-09-11T10:31:07.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-09-13T15:12:30.000Z (over 1 year ago)
- Last Synced: 2025-01-21T20:48:47.350Z (4 months ago)
- Language: Nextflow
- Size: 450 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Circall_quant: fast circRNA quantification with Quasi-mapping
## 1. Introduction
This a a portable quantification module of cscQTL used for fast circRNA quantification with known highly confident circRNA candidates.
## 2. Installation
### 2.0 Hardware requirement
The pipeline requires at least a linux system with 32 CPUs and 32GB of RAM to run. You may customize the requiment in the main.nf but generally not recommended.
### 2.1 Dependency
Since Circall_quant is implemted with Nextflow (DSL2), you would need Nextflow to run it. Further information to install Nextflow can be found on its home page:[https://www.nextflow.io/](https://www.nextflow.io/)
For tool dependency, I have placed all dependencies in their corresponding container, so you would need to run with Docker or Singularity.
The default desgins of Circall_quant is running with either Docker using a single machine (**-profile standard**) or with sigularity using slurm HPC(**-profile cluster**), you may need to change the **nextflow.config** to adapt to the your system.
Further customization, I recommend to consult Nextflow homepage: [https://www.nextflow.io/docs/latest/config.html](https://www.nextflow.io/docs/latest/config.html)
### 2.2 Clone the pipeline
```sh
git clone https://github.com/datngu/circall_quant.git
```
## 3. Parameters
| Parameters | Description | Default setting |
| :------------------ | :------------------------------------------------------------------------------------------------------------------ | :------------------------------------- |
| genome | genome in fasta format | $baseDir/data/ref/genome.fa |
| cdna | transcripts (cDNA) in fasta format | $baseDir/data/ref/cdna.fa |
| annotation | ensembl annotation in gtf format | $baseDir/data/ref/annotation.gtf |
| reads | ribo minus RNA seq reads in fastq.gz format | $baseDir/data/reads/\*\_{1,2}.fastq.gz |
| circRNA | circRNA candidate list | $baseDir/data/circRNA_list.txt |
| trace\_dir | directory for tracing output - all intermediate files in the analyses will be soft-linked here - used for debugging | $baseDir/trace\_dir |
| outdir | directory of output | $baseDir/results |
## 4. Test example
## 5. License
Circall_quant uses GNU General Public License GPL-3.
## 6. Reference
Dat Thanh Nguyen. 2023. "An integrative framework for circular RNA quantitative trait locus discovery with application in human T cells." bioRxiv 2023.03.22.533756; doi: https://doi.org/10.1101/2023.03.22.533756
Nguyen, D. T., Trac, Q. T., Nguyen, T. H., Nguyen, H. N., Ohad, N., Pawitan, Y., & Vu, T. N. (2021). Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data. BMC bioinformatics, 22, 1-18.