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Hello,
I encountered the following error during the execution of my circular RNA analysis pipeline:
```bash
Indexing .bam file...
open: No such file or directory
[bam_index_build2] fail to op…
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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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### Description of the bug
I tried to run the test profile with `nextflow run nf-core/circrna -profile test,docker --outdir ./test` but get the error below. As both the test and test_full profiles us…
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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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Hi everyone
Currently, I am analyzing circRNAs from an RNA-Seq dataset using CIRI2 tools, following the steps outlined in the CIRI-cookbook. Here's how I have proceeded:
1. Checked the FastQC of t…
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### Description of the bug
Hello,
I encountered this error using DCC.
### Command used and terminal output
```console
nextflow pull nf-core/circrna
nextflow run nf-core/circrna \
-r dev \
…
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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…
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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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### 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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Hey,
Thanks for sharing this amazing tool!
I found that **chrMT** appears in the .bed and .junction files, but not in the final counts table.
I was wondering if there is any way to help me gen…