Question: circRNA-Seq analysis tools
0
gravatar for Ömer An
2.3 years ago by
Ömer An220
Singapore
Ömer An220 wrote:

Hello,

I have circRNA-Seq samples and I am looking for tools to identify the circRNAs in these samples.

In circRNA-Seq, all linear form of RNAs are degraded to enrich the circRNAs, which is still in principle RNA-Seq.

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?

Can you suggest me the best tools/approaches to detect the circRNAs from the circRNA-Seq data?

circrna circrna-seq • 1.1k views
ADD COMMENTlink modified 2.3 years ago by IP700 • written 2.3 years ago by Ömer An220
1
gravatar for IP
2.3 years ago by
IP700
Denmark/University of Copenagen
IP700 wrote:

Hi!

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!

ADD COMMENTlink modified 7 months ago by Kevin Blighe67k • written 2.3 years ago by IP700
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