I am doing circDNA prediction, as there is not softwere yet available. So I want to generate pipeline for it. Can anybody tell me how to setup pipeline for this type of data. I have tried CIRI but it detected circRNA, not circDNA. I need circDNA.
We have publish today on biorvix a preprint with a new algorithm for circular DNA detection.
The code is now publicly available via github (https://github.com/iprada/Circle-Map) and it contains a step-by-step tutorial (https://github.com/iprada/Circle-Map/wiki/Tutorial:-Identification-of-circular-DNA-using-Circle-Map-Realign) explaining how to go from the raw data to interpretable results.
I hope it helps!
Thanks for using Circle-Map.
The reason you are getting the error is because your system is using bash and not python to interpret the code. And of course, bash does not understand python. I think that this error was caused because the source code was directly downloaded from github instead of using the installations recipes.
I recommend this two solutions:
I did create easy installation recipes for pip and conda, so that the software and its dependencies where easy to install. You can install the software using pip with the following command ( needs python >=3):
python -m pip install Circle-Map
And with conda using a similar flavour:
conda install -c bioconda circle-map
This should solve your issue. Let me know if this helps,