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I've tried testing two of your workflows and get the following error in both:
nextflow run nf-core/rnaseq -r 1.4.2 -profile test,singularity
nextflow run nf-core/smrnaseq -r 1.0.0 -profile test,si…
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Hi - Thank you for making this analysis tool available. I am running a analysis on a genome of a bacterial environmental isolate. Similar to another issue the ksd command results in multiple errors. I…
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Hi
I run STAR for single-end reads as following:
```
STAR --runMode alignReads \
--twopassMode Basic \
--runThreadN {threads} \
--genomeDir {input.index} \
--sjdbGTFfile {input.gtf} \
…
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If I run sc_exon_mapping, sc_demultiplex and sc_gene_counting separately, in "UMI_duplication_count.csv" file, I get duplication number 1's count 0. This does not happen when I run sc_count_aligned_ba…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/SaskiaFreytag/schex
Confirm the following by edit…
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Hi David (and/or anyone who knows the answer to my questions),
I've managed to run Orthofinder on a 51-taxon dataset (ferns!), but am having trouble understanding the output. I don't see any indica…
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CNV
1. We have ControlFreeC and CNVkit. CNVkit output is VCF – do users want raw output for these or should we convert ControlFreeC output to VCF, then annotate all with AnnotSV (which is what we are…
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Genes are duplicated in the dict returned by the GenomeGeneRetrieveView and in the g.genes element in the visualization. This duplication is due to both a "gene" feature and a "CDS" feature of each ge…
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To improve reproducibility, use of external data sources (e.g. APIs, databases, git repositories) in the pipeline needs to be removed. Instead, there will be a pre-generation step where the external s…
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I would like some clarification on how to interpret my GARD results.
I ran GARD a Drosophila gene underwent duplication in some lineages, and I included both the orthologs across Drosophila as wel…