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Hi! Do you have a list with a quick description for the file formats that can be used for the barcode whitelist, please? (I used a simple .txt file with a cell barcode on each line.)
Thank you very m…
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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
We have used `Kit : 10X Genomics Next GEM Single Cell 5' v2 (Dual Index)` for `two healthy PBMCs` as a test experiment before investing on our main design
Now, for running the main experiment…
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Hi !
I have an error when I use a FASTQ file as input, I do not understand why... I use the docker image from singularity.
I ran that :
```bash
singularity run \
src.sif toulligqc \
-a sequen…
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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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According to the example config files, I believe one should specify `readPaths` the parameter to process multiple samples at once (not the `--reads` option). It would be great if this feature is expli…
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I can print a receipt that has 4 columns ?
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Hi,
Thank you for developing SCENIC+. I am excited to use it.
When I want to use compute_qc_stats(), I get below traceback.
```
AttributeError Traceback (most recent…
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Hello,
Thank you for such a great tool!
I have a quick question about the UMI counts per barcode after running `remove-background`. I noticed that the number of UMIs in my samples went up greatl…
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I would like to use the scRNAseq files posted on GEO, GSE153835. However, I'm having some trouble understanding where these files fit in the R downstream analysis posted here on github. I see 4 file…