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I need to use a demuxlet to demultiplex the data generated by BD Rhapsody platform.
I checked the --tag-umi and --tag-group formats of the data generated by Bhapsody,
but I don't know how to enter …
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Hello, I am trying to reproduce some of the results from the paper. I am currently trying to separate all cell line datasets. I have been able to follow the instructions in the supplementary section t…
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Hello,
Thank you for developing such a wonderful method.
Recently, I attempted to execute somatic variant calling from scRNA-seq data, following the step-by-step instructions provided on your GitHub…
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Dear respected author,
Hello! I am thrilled and deeply inspired after reading your work, as I am currently seeking methods to distinguish diploid and tetraploid cells in plant scRNA-seq data. I w…
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This issue tracks changes we should implement as noticed during June 2024's Intro scRNA-seq training.
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Hi Salmon team
Are there plans afoot to support quantification of scRNA-seq data with unique molecular identifiers (UMIs)? UMIs are very commonly used in scRNA-seq data now, and correct quantificatio…
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Hi !
Thanks for the amazing pipeline! I remember reading before, but couldn't find the details now, so here I am. What is the number in the TAR read before _0 or after the strand? Is it the number of…
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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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[Single-cell RNA-seq denoising using a deep count autoencoder](https://www.nature.com/articles/s41467-018-07931-2#ref-CR33)
> **Denoising enables discovery of subtle cellular phenotypes**
> Aft…
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Hi,
I am processing an scRNA-seq dataset containing 14 samples. For each sample, I performed the standard QC filtering based on nFeatures and mitochondrial gene percentage, followed by the identifi…