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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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Could DCC get f-circRNA ? #88

Closed gnilihzeux closed 3 years ago

gnilihzeux commented 3 years ago

Dear author,

It's ok for DCC to detect some circRNAs within multiple genes, but could it work for inter-chromsomes circRNAs, like those derived from fusion-genes such as PAX3-FOXO1?

BTW, I'd found a specialized program Fcirc for f-circRNA.

Thanks.

tjakobi commented 3 years ago

Dear @gnilihzeux,

thank you for your interest in DCC.

DCC was not designed for the purpose you outlined.

Inter-chromsomes circRNAs should be automatically filtered out by DCC if they are recognized as those.

You might be able to see fusion candidates when not using -fg filter option, but I have doubts that this would work between different chromosomes.

Fcirc in this case might be the better choice.

Cheers, Tobias

gnilihzeux commented 3 years ago

Thank you. I'd try another tool fcirc.