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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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I analyzed 12 sets of paired end reads with CIRI-full pipeline and tried to run CIRI-vis on each of them. 11 samples worked fine but for the 12th sample, CIRI-vis generates the circRNA plots and list …
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I had an error with CIRIquant. starting from `Warning: Empty fasta file: '/oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-1-R_index.fa'` then `(ERR): "/oasis/tscc/scratch/hsher/circSTAMP_pipe…
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Hi,
I have an issue running an analysis. I prepared the necessary files in the following directory structure:
.
└── test
├── input
│ ├── backsplice_gene_name.txt
│ ├── hg38.fa
…
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Hi guys,
When I ran the command:
```sh
CIRIquant --config circ_quant_cfg.yaml -1 sampleA.R1.fq.gz -2 sampleA.R2.fq.gz --bam sampleA_sorted.bam -o ./sampleA -p sampleA -t 8 --bed CircRNAs.bed -e…
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Hello,
*******1st question*****
I am trying to use the peOverlapNbasesMin option and i need to generate Chimeric.out.junction for further analysis with circexplorer. Here is my command:
$STAR/so…
npont updated
11 months ago
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Hi,
A couple of questions:
- Do any dep files exist for mouse / how to generate these?
- I see Execution halted, but completed results files. Whats going on there?
Best wishes
Alistair
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How exactly does COMPSRA determine if a read maps to a circRNA? Does it specifically consider only reads that map to the splice junction? Otherwise, reads from linear mRNAs that map to an exonic seque…
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Hi egaffo, thanks for the prompt reply. I tried the new docker but I keep having a similar error:
user@NGS:~/CirComPara$ sudo docker run -u `id -u` --rm -it -v $(pwd):/data egaffo/circompara2:v0.…
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I am not looking to do differential expression so I did not open the DE module.
However, I would still like to normalize the count data with transcript length.
Is there any way to obtain this f…