search

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
6 stars 9 forks source link

removed debug print from output #32

Open selkovjr opened 8 months ago

selkovjr commented 8 months ago

This print call in AssembleJSeq.py was contaminated one of the intermediate outputs, leading to the ivalid (empty) novoindex:

print(common_IDs)

This results in this error condition at the following step does not appear to be a valid novoindex

chiangtw commented 8 months ago

Hi, Thank you for trying to report bugs for NCLscan, but the print() call was not appeared in the original file.

https://github.com/TreesLab/NCLscan/pull/32/files

Still, thanks for the kindly report!

Best, tw

selkovjr commented 8 months ago

Interesting. Has it ever been there? I first cloned the repo a couple years ago and struggled to get past that point, not knowing what caused the empty output. I only found it recently by tracing and mapping every step of the workflow, with the same input.

Removing that line made it run to the end. Maybe my former self put it in; I can't remember. Sorry about the noise if that's what I did. But then there is a mystery of what broke the workflow originally.

Since we are on the topic (almost), do you see an easy way to discover circRNAs that do not result from canonical splicing? I have a sample with a massive amount of RNA concatemer made of a fragment of ROS1 exon 37. The repeat unit is a fraction of that exon that does not include a splice site. I can only discover such things by clicking around in a browser.

Thank you,

--Gene

On Tue, 12 Dec 2023 at 07:26, Tai-Wei Chiang @.***> wrote:

Hi, Thank you for trying to report bugs for NCLscan, but the print() call was not appeared in the original file.

https://github.com/TreesLab/NCLscan/pull/32/files

Still, thanks for the kindly report!

Best, tw

— Reply to this email directly, view it on GitHub https://github.com/TreesLab/NCLscan/pull/32#issuecomment-1851436066, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADRV2A5QOBEBHS3ZKHO3NTYJABKVAVCNFSM6AAAAABAQF6W6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJRGQZTMMBWGY . You are receiving this because you authored the thread.Message ID: @.***>