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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,
is there any option to save mapped reads? So, we could display the circRNA reads on IGV.
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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,
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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Hi Kipp,
I have met another issue when I analyzed my data (stranded total RNA-Seq) from FASTQ files. Only 9 circRNAs were detected but previously using BAMs as the starting point I found more than …
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I wonder if it is possible to include a new circRNA database (such as circAtlas). And in case of yes, which information it will be needed for that and which are the steps.
Thanks!
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Hi egaffo,
I'm trying to run circompara on my samples, but I got the following error:
finished circRNA detection from file samples/S1/processings/circRNAs/star_out/Chimeric.out.junction
dcc_fix_s…
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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 try to use Clirc and I have a problem in the first step. When I try to extract circRNA sequences from my file with coordinates and reference genome that were used to detect circRNA i have the follow…
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Dear Professor,
Hello, thank you for your team's development of CIRIquant, an excellent tool. I have a question that needs your help. I want to know how to obtain the mature full-length sequence of…