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Dear egaffo,
The "combined_circrnas.gtf" generated by CirComPara in circRNA_collection step showed confused results.
For example, the table below is simplified from a "combined_circrnas.gtf" file, …
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Dear Enrico,
Sorry to trouble you for a while. I have another question. I have run CirComPara with two methods findcirc and circexplorer, several folders and a number of output files are generated.…
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DCC crashes when using the following command line:
```
DCC @samplesheet -mt1 @mate1 -mt2 @mate2 -T 8 -D -N -an
/data/yaoyh/circRNA/GTF_file/gencode.v26.annotation.gtf -Pi -F -fg -G -A
/data/yaoyh/…
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Hi,
I met a problem when using the script getcircfasta and the DCC output CircCoordinates to extract the circRNA sequences for further detection of miRNA binding sites on these sequences. The numb…
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CIRCexplorer parameters: /usr/local/bin/CIRCexplorer2 annotate -r ref.txt -g ref.fa circ
Start CIRCexplorer2 annotate at 11:44:56
Start to annotate fusion junctions...
Annotated 0 fusion junctions!…
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I have run FUCHS [https://github.com/dieterich-lab/FUCHS/commit/ec9fd7218254da32d9764052617547491d38797e](url)
on our long RNA-seq data sets.
The mate status (e.g. 1746_A.mate_status.txt) of all r…
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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 construct…
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hi author:
The below words quoted from your website about characterization of Circular RNA Alternative Splicing
"It requires alignment results (set using -a) of poly(A)+ RNA-seq derived from the same…
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When I run DCC, I get an error with pybedtools groupby:
python2.7 /home/ehutchins/tools/DCC/DCC/main.py @chimeric_junctions -mt1 @chimeric_junctions_mate1 -mt2 @chimeric_junctions_mate2 -D -N -temp …