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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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Is it possible to retrieve the pseudo-references?? #6

Closed Aufiero closed 8 years ago

Aufiero commented 8 years ago

Dear colleagues, I used NCLscan to detect circRNA molecules. From what I understood this tool uses pseudo-references as a strategy to detect this kind of molecules. All pseudo reference are constructed where the exons are topologically inconsistent with the reference genome. A pseudo-reference is regarded as a circRNA candidate if it has at least one reads that maps to its NCLjuntion sites. I had a look at the output files, but I didn't find any file containing the pseudo-references regarded as a circRNAs, maybe I missed it, so I was wondering is there such a file? Thanks, S

chiangtw commented 8 years ago

Hi,

Please check the file "[Project].JS2.fa", and you can use the candidate IDs(1st column of "[Project].result.tmp3") to get the needed sequences.

Note. The pseudo-references used in NCLscan are just for the detection of the NCL junction sites.