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### Description of the bug
Hello,
I am trying to run nf-core/circRNA on sncRNA samples, and I encountered an error during the annotation part for some of the samples. I noticed that the samples wi…
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### Description of the bug
Hello,
I recently encountered an error while running CIRIquant when providing a specific GTF file. Other tools, such as circRNA_finder, run without any issues and perfor…
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How exactly does COMPSRA determine if a read maps to a circRNA? Does it specifically consider only reads that map to the splice junction? Otherwise, reads from linear mRNAs that map to an exonic seque…
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Hi,
I am trying to run the isocircPlot script and am getting an error with bedtools and I am not really sure what to do in this situation. Do you think it has to do with the version of bedtools or …
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I see that there exist circular RNA support in Sailfish ( http://www.rna-seqblog.com/tag/sailfish-cir/ ), maybe it will be beneficial to see a Salmon port of it?
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Hi,
Thanks for a great tool for the analysis of circRNA-seq. I quantify the circRNA-seq data with CIRIquant, but I do not know which of the following ways to construct the index for the circRNA-seq…
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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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I tried both circtools detect v1.3.1 and DCC v0.5.0 using this command in Snakemake:
I only used one sample, paired-end read
```
circtools detect {input.samplesheet} \
-mt1 {input.…
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Hi!
I have two questions:
1. There is no explenation what exacly mean column names in quant.sf file. Do you have such information?
2. When i try to count expected number of reads arising from s…
KateK updated
5 years ago
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Hi, I found another bug(?) in your code:
during the process to sort the circRNA to output by junction reads count,
since there is no header in your **circRNA_list_temp.txt** file, so there is no need…