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### Description of the bug
The error appear when nf-core/scrnaseq is launched with any aligner at the emptydrop step. The pipeline is labelled as completed but with errors as it failed with the outp…
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Hi Alex,
I have a question about best practices for dealing with multi-mapping reads in scRNA-seq data analysis, particularly when looking at transposable elements (TEs). Due to the nature of TEs,…
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### Description of the bug
nf-core/scrnaseq test using conda fails with the following error message. Fetched from '.nextflow.log'. Thanks!
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONV…
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Hi
I am getting the following error when aligning my 5' 10X CRISPR scRNAseq data using alevin fry:
/mnt/dv/wid/projects6/Roy-singlecell3/sridharanlab2/data/perturb-seq_on_reprogramming/fastq/G…
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One file per sample is WES T-N.
Multiple samples per file is scRNASeq.
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### Applies To
- [X] Notebooks (.ipynb files)
- [ ] Interactive Window and\/or Cell Scripts (.py files with \#%% markers)
### What happened?
Using the following kernel:
```bash
mamba create -n …
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Hi,
I'm working on the integration of human and zebrafish scRNAseq data, refering to this benchmarking strategy and code, I got a overintegrated umap in samap analysis, yet a Unintegrated umap in sc…
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### Description of the bug
Hello,
a previous run only providing the unfiltered data worked fine.
I have now added the filtered data from a rerun of scrnaseq just to increase my options.
That addit…
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### Description of feature
I am currently looking into using scrnaseq for a clinical trial. In our setup we have GEX, FB, and VDJ data for several patients which are hashed using Totalseq-C. Curren…
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Hi. This is a very useful tool. I'm wondering if this tool can be applied to Parse Biosciences scRNAseq technology. Are you thinking about doing a tutorial about this? Thank you very much.