Dockerized CirComPara

CirComPara: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data.¹

Usage

Docker pull command:

docker pull egaffo/circompara-docker

Run command example:

docker run --rm -it -v $(pwd):/data egaffo/circompara-docker

Mind that all files must be in the current directory and that paths in meta.csv and vars.py must be relative to the container /data directory. For instance, using the test data, you have to copy the annotation and reads directories into the analysis directory. Then, meta.csv will be as follows:

file,sample,condition,adapter  
/data/reads/readsA_1.fastq.gz,sample_A,A,/CirComPara/tools/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa  
/data/reads/readsA_2.fastq.gz,sample_A,A,/CirComPara/tools/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa  
/data/reads/readsB_1.fastq.gz,sample_B,B,/CirComPara/tools/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa  
/data/reads/readsB_2.fastq.gz,sample_B,B,/CirComPara/tools/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa  

and vars.py:

META            = "meta.csv"
GENOME_FASTA    = '/data/annotation/CFLAR_HIPK3.fa'
ANNOTATION      = '/data/annotation/CFLAR_HIPK3.gtf' 

The results will be owned by root. If you want the container to give your user permissions try to use the "-u id -u" workaround:

docker run -u `id -u` --rm -it -v $(pwd):/data egaffo/circompara-docker

How to cite

If you used the docker image of CirComPara for your analysis, please add the following citation to your references:

Footnotes

1. Gaffo, E., Bonizzato, A., Kronnie, G. te & Bortoluzzi, S. CirComPara: A Multi‐Method Comparative Bioinformatics Pipeline to Detect and Study circRNAs from RNA‐seq Data. Non-Coding RNA 3, 8 (2017). http://www.mdpi.com/2311-553X/3/1/8 ↩