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Current runs show circular RNA candidates that are located within an annotated gene but on the different strand. Is this biological reality or maybe an error in the stranded workflow?
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In Virtool reference, name is Cherry leaf scorch viroid. Name on Taxonomy DB is [Cherry leaf scorch small circular viroid-like RNA 1](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=142342…
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First of all, thank you for making these scripts available. This is not really an issue, is more a request for clarification of the tool's output. I am witting here to that others with the same proble…
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Another way to select for differential expression of backsplicing junction is to compare with the expression of the linear junction between the two exons.
Refer: Rybak-Wolf et al. 2015. Circular RNAs…
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Hi,
I have done the circular RNA prediction, the files CircCoordinates,CircRNACount,CircSkipJunctions and LinearCount generated.
The CircRNACount file has duplicate rowname with different expression…
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Dear Dr. Christina Huan Shi,
Thank you for this great software. This software is very helpful and incredibly fast. But when I run it using my own data, I got a result unexpectedly.
I ran psir…
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hey i m using circexplorer2 for circular RNA detection in solanum lycopersicum for that how may I generate the .refFlat file for solanum lycopersicum or ref.txt file so that i can pass that step.
i …
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I'm also getting a similar error for bulk-RNA data,
```
> bam_files
MCAO1 MCAO3 MCAO4 Shame1
"../…
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Hi again,
I would like to know if the number of times a circRNA is repeated in each read (which I think you call CCS copy number) is reported somewhere in the output of CIRILONG. Mi idea is to get …
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Hi SO,
There are a few tweaks needed for the entry for circular_ncRNA, originally discussed on #490.
http://www.sequenceontology.org/browser/current_svn/term/SO:0002291
1. For synonyms, convert "…