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Hello,
I was wondering if you can realign the scATAC-seq data using the newest version of cellranger atac since the deduplication has changed the output fragments significantly (better)?
Best,
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I'm currently working on applying PASTA, and I'm having trouble creating a fragments TSV file using Sinto. I've looked through the documentation and searched online, but I'm still not clear on how to …
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Hey,
I am using https://stuartlab.org/signac/articles/pbmc_multiomic on a multiome dataset.
I have 5 samples with 5 different fragment files stored in a folder called "Signac_fragpath" ,
Here is…
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Hi @satijalab!
Thanks for developing this great tool, which makes it very easy to annotate new single-cell datasets.
I'm the first author of the paper [An Atlas of Cells in the Human Tonsil](htt…
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Hello,
I converted my Seurat objects (scRNA + scATAC) to a Liger object using the "seuratToLiger" function:
data
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Good day!
First of all congrats on the paper! looking forward to try it on our dataset.
We have a dataset where we have integrated paired (truly multiome data) and unpaired (scRNA and scATAC in…
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Hi there!
Thanks so much for this wonderful ATAC resource, I have a question for you that may be simple. Rather inexperienced in the land of python, so any guidance you could provide would be gratef…
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https://mp.weixin.qq.com/s/gxrbnunooi6Riv22BdIbcw
ixxmu updated
11 months ago
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Ingest Seq Receive Library script has errors:
Possible spreadsheet error:
/opt/l7esp/data/extensions/client/lib/python3.9/site-packages/openpyxl/worksheet/_reader.py:312: UserWarning: Data Validatio…
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Hi @jphe, thank you for developing the useful package. I wanted to apply scTE to scATAC-seq data but the output .csv file shows only 960 features, all of which seem to be TEs (no genes). It also appea…