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Hello,
Thank you for developing such an innovative package! I've been trying to run `CITE-seq-Count` on my 10X V3 data, but keep on getting 100% unmapped returned.
This is the command I used:
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Hi,
Thanks for developing this great tool. I just have 2 questions regarding CITE-seq-Count.
Question1:
So, I have a multimodal scRNAseq dataset in which both CITEseq and Hashtag antibodies wer…
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From our tutorial
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Hi,
Thanks for the excellent method for CITE-seq!
I find the vignettes from "https://cran.r-project.org/web/packages/dsb/vignettes/end_to_end_workflow.html" only deal with one sample.
If I have mul…
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I'm trying to understand how to run the `cite-seq-count` with data made with the 10x protocol for Next GEM Single Cell 3' HT v3.1.
Reading the user manual for the tool, I should run the command wit…
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I'm having issue running CITE-seq-Count because it's taking up too much memory. I tried running it on a cluster and even that got timed out.
Start Time = 12/06/2021 23:26:26.956
End Time …
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Hello I used seurat to proess a CITE-seq dataset, upon looking at antibody expression, the results are somewhat strange. That is most antibodies are expressed by most cell types/clusters. Although the…
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When I use "CITE-seq-Count-R1./ SRR13724311_S1_L001_R1_001.fastq.gz-R2 SRR13724311_S1_L001_R2_001.fastq.gz-t Cmca9_tag_list_utf8.cfa-cbf 1-cbl 16-umif 17-umil 28 -cells 10000-o OUTFOLDER "is always no…
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Hi,
I was wondering if you could help me with the following urgent issue: our protein lane has 34k cells (after mapping with CITE-seq-Count using -cells option, no whitelist), RNA lane has 11k cell…
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Joana provides a good description with implementation ideas:
Here’s what I am thinking:
We want to cluster based on the gene expression and then color the cells based on the sequence barcode for…