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TreesLab / NCLscan

We have developed a new pipeline, NCLscan, which is rather advantageous in the identification of both intragenic and intergenic "non-co-linear" (NCL) transcripts (fusion, trans-splicing, and circular RNA) from paired-end RNA-seq data.
MIT License
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NCLscan and unpaired read data? #20

Open wolfgangrumpf opened 5 years ago

wolfgangrumpf commented 5 years ago

Is there a way to run NCLscan on non-paired-read data (e.g. PacBio output)?

chenchiaying commented 5 years ago

Hi,

NCLscan cannot apply to long reads.

But, our team now is developing another NCL tool on long-reads (PacBio/Nanopore). This new tool still needs a non-co-linear result (fusion, trans-splicing, and circular RNAs) from short-reads and looks for full-length of a non-co-linear event using long-reads.

Chia-Ying

wolfgangrumpf commented 5 years ago

That's great news - do you need testers? When do you expect the tool to be ready?

chenchiaying commented 5 years ago

Yes, we do need testers. Thanks for your generous help. The longNCL tool is planning to release in GitHub within 2 weeks. I will let you know when it is ready. Keep in touch:)

Chia-Ying