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### Description of feature
When running the pipeline with `--save_reference`, currently only the STAR index is saved. It would be useful to also include the Salmon and RSEM index inside the `./geno…
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### Description of the bug
I don't have interval file , I hope use GATK CombineGVCFs options , I would like to ask how to use this feature , thank you!
### Command used and terminal output
```conso…
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Hi Felix
I have some custom tagged bam files where the first 14 tags are the same as bismark output, but the XR and XG tags are missing. Is it possible to extract the methylation calls using bismar…
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### Description of the bug
I am running nf-core/rnaseq with the following command:
```
nextflow run nf-core/rnaseq
-r 3.14.0
-profile docker
--input /media/unidad/Expansion/Raw_…
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HI, I have downloaded couple of gbff files but when running this wonderful pipeline I have this error message:
##### Infering colinearity from protein-coding gene clusters
The number of annotation…
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- [x] **Moving "scary" warning messages to the verbose option**
The following warning message pair (which addresses the same issue) is only one of hundreds of similar warning messages that occur wh…
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I am working with a set of genes that got scattered across the genome of fishes and I am looking for a way to compare such scaffolds to help define syntenic/ancestral regions shared across them. Howev…
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Hello,
I am using bismark to prep my files before using Methylkit. I have run FastQC on all my data and then trimmed them using Trim Galore! I was able to successfully run the genome preparations as…
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Hello,
I have a question: according to Oxford nanopore their last cells produce very accurate reads. Does "map-ont" still work as the best setting to map those reads? I am asking because the manual…
ghost updated
1 month ago
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We're interested in quantifying isoform specific stability with a custom set of 3'UTRs
If we were to tweak the bam2bakR pipeline, supplementing a custom set of isoforms as separate ‘genes’ to a sta…