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bioinfo-biols / CIRI-long

Circular RNA Identification for Nanopore Sequencing
https://ciri-cookbook.readthedocs.io
MIT License
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Non-canonical splice sites #10

Closed mmaitenat closed 2 years ago

mmaitenat commented 2 years ago

Hi again,

I would like CIRI-long not to rely on the canonical GT/AG splice signal only. However, when I run the tool both with and without the --canonical argument, the results are the same. If I understood correctly, the --canonical option is always set to TRUE. Is it possible to disable it so that non-canonical ones are also considered?

Thanks,

Maitena.

Kevinzjy commented 2 years ago

Hi @mmaitenat, the '--canonical' option is not effective. Considering the high-error rate of nanopore reads, it's more appropriate to use defined splicing signals rather than perform de novo alignment. Here's the instructions to modify splice signal sequences in CIRI-long: https://ciri-cookbook.readthedocs.io/en/latest/CIRI-long_2_usage.html#using-non-canonical-splice-signals