2.5 years ago by
Denmark/University of Copenagen
To answer your questions:
There are plenty of tools to detect circRNAs from RNA-Seq data such as
CIRCexplorer2 or just using STAR alignment with chimeric reads option
but do they still apply to circRNA-Seq in my case?
tools like CIRCexplorer2 definitively work for circRNA enriched RNA-seq samples. If you are in doubt about what tool to use, I have got good results with STAR-> CIRCexplorer2 in the past, and both STAR and CIRCexplorer2 are well documented and are easy to use.
Can you suggest me the best tools/approaches to detect the circRNAs
from the circRNA-Seq data?
There are plenty of tools for working with circRNA now, and the best tool will depend on the scientific questions you want to asnwer with your data, which species you work on and a large etc. There is a really good evaluation of circRNA detection tools who was published last year., This will help you a lot to decide which tool is the best depending your analysis.
Best of luck and good science!