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The metadata file used to create my phyloseq object has a couple spelling errors, and now it is recognizing one sample name as two sample names. Example: the variable "tissue type" contains the catego…
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For all of the quantification methods I have tested (`Gene` and `GeneFull`) the `barcodes.tsv` file in the `Solo.out//raw/` folder does not reflect `CB` whitelisting. Instead it is an exact copy of t…
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Hi, thank you for the great tool!
I am experiencing some issues loading paired single cell data.
I have csvs for each of my samples that have a barcode column and cdr3, v, and j (d coverage was l…
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This will be the first step of the pipeline.
Implement the following software into a Snakemake pipeline to QC nanopore data
- [x] https://github.com/wdecoster/NanoPlot
- [ ] https://github.com/Genom…
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Hi,
I am trying to use the STARsolo function to process full-length 10X cDNA reads. I parsed the data into read pairs (One containing the actual (~1200nt) read, the other the 10X cell barcode and …
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Hello Alex,
First of all - thank you so much for developing STAR. I (like many others) find incredibly useful and easy to work with. Cool, too!
That said, I have been having trouble mapping some…
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I can print a receipt that has 4 columns ?
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Have you used bcr_dist with non 10X data? I see you can load a "BD" file, I am not familiar with this format...
Hoping to be able to map the emerging AIRR Clone format (https://github.com/airr-comm…
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Hi Aaron,
I used `read10xCounts(..., type = "HDF5")` to load a HDF5 file from CellRanger v3.
I was surprised to get an error when I then ran `scater::calculateQCMetrics()` on the result.
Ultimately…
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I tried pulling the singularity image of this on a Linux-based (Rocky Linux 8.5) computer cluster. I got a couple of warnings but wasn't sure if they were normal.
```
$ singularity pull --arch amd…