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Hi,
thank you for this great tool.
I am running spacemake for an openST data and encountering the following Error when running `spacemake run --cores 8`:
```Error
KeyError in line 286 of /ho…
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Hi,
I encountered an error after the ReduceGTF step in the pipeline - Invalid GTF line and missing transcript_name.
I am running it on Arabidopsis data, so I changed the rule that fetches the an…
vuzun updated
4 years ago
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Overall strategy: sample all reads of cells from a list of cell-ids with known cell-type
- a simple database (e.g. sqlite, even a flat textfile could do it) that stores: cell-id, path to fastqs, ce…
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**Is your feature request related to a problem? Please describe.**
The use of submodules is valuable for modularity and keeping an organized project structure with some modules potentially working on…
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When I try to run vib-singlecell-nf /vsn-pipelines example ( the single-sample) configured to use singularity I get this error
**_Invalid method `doCall` invocation with arguments: on _closure15 ty…
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https://github.com/alexdobin/STAR/releases/tag/2.7.0a
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Hello everyone,
today I ran into some problems in generating the metadata for the single-cell pipeline. I got an unclear error message in the create_refFlat rule when running dropSeqPipe on a Gallu…
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Figure out tagging with gene name, location
Choose a custom feature assignment method or DropSeqTools or maybe umitools?
Check if dropseq tools is testing their code
AC:
Analysis
Choose a feature ass…
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Resolving multi aligned reads by utilizing UMIs for correction. You could potentially observe more features if this is done. This has the potential to reduce generation costs if we are able to reduce …
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In the optimus zarr output, the `gene_id` array contains gene names. The other pipelines use gene ids, which is what the matrix service is expecting. Also, gene ids are unique whereas i think the gene…