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Hi,
I have been using MATES for short read data recently and I wanted to try ATAC data only, however, I am not sure how to process the data.
First, to keep multi mapping information, is it necessary…
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I've been using `ProjecTILs` and the CD4/CD8 human T cell reference atlases in some scRNA-seq work lately and it has been very useful for us. I wonder whether you or @ncborcherding (via https://github…
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Hello, I want to use scATAC-seq dataset to deconvolute 10x Visium dataset, is it feasible?
When I prepare anndata for the regression model, some warings appeared as follows:
cell2location.models.R…
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I found it very slow when I used a 30k scATACK-seq data with top 50k peaks, how many peaks should I use for the input of scATAC-seq data?
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Hi, I have some unpaired scRNA-seq and scATAC-seq data, they are sequencing the same samples, but in separate scRNA-seq and scATAC-seq assays, so the cell barcodes are different in these datasets. How…
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Hi there,
Thanks for providing such an interesting tool for the research community.
I am testing the pipeline on scATAC-seq tumor samples only. How to work around "Step2. Unbiased segmentation ba…
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Hello,
I am using SComatic to compute germline genotypes for known variants in 10x Multiome datasets.
I can get the SingleCellGenotype of scRNA-seq data.
when I run SingleCellGenotype.py on scAT…
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Congratulations on the wonderful-looking update on VIA.
This is my first time trying to use VIA (or StaVia), and it seems like the tutorial for [scATAC-seq Hematopoiesis] link is not working corre…
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Can this platform be used for shallow scATAC-seq data? I have output from cellranger atac count pipeline. How can I generate doubletD inputs from this?
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Hi,
I am trying to download the [scATAC-seq data](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178324) and remap it to hg38. I just wanted to double check that I got the experimental design …