circrna
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nf-core
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
Hey, this PR addresses 4 things: 1. Exclude overlong circRNAs from quantification as psirc-quant throws an error otherwise 2. Use only the circRNAs which pass the detection majority vote in...
Do not merge! This is a PR of dev compared to first release for whole-pipeline reviewing purposes. Comments can be copied over to #66 for safety if necessary and changes...
### Description of feature Currently there is only a custom image available via dockerhub. We should find a cleaner solution, most likely via a bioconda recipe.
v1.0.0
DSL2 version of nf-core/circrna. A few minor comments on the linting warnings: 1. I need some assistance configuring the full AWS test dataset. The data can be accessed via SRA,...
### Description of the bug Hiya, thank you for the work on the pipeline! Currently, when I try to run the pipeline using my own (paired-end) data, it seems that...
### Description of feature Currently, only the BSJs are detected and quantified, without knowing the exact sequences. There are several tools which can obtain the full length circRNA sequence from...
### Description of feature This should be an optional column in the samplesheet. If available, it should be used in detection tools like `CIRI`. The following things need to be...
Recently, @nictru updated the annotation pipeline (with #95), improving the overall performance. This should also be applied to the DIFFERENTIAL_EXPRESSION:PARENT_GENE process
### Description of feature Checking the detected circRNAs for their coding potential could open an additional perspective on deciphering the function of circRNAs. [This tool](https://pubmed.ncbi.nlm.nih.gov/28521017/) was suggested to me for...
### Description of the bug When using STAR indices from iGenomes, the versions are partly not compatible with the STAR version used by the pipeline. A workaround is setting manually...