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Very useful and easy to use tool!
I wanted to ask if DoubletDecon can be repurposed for scATAC-seq doublet detection. Theoretically, you could run DoubletDecon on the **gene activity matrix** crea…
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Hello.
I have 4 snATAC-seq samples from the DNBSEQ-T7 platform, and for each sample, they are mixed with multiple cell lines. For R1, the read length is 50bp, and for R2, the read length is 70bp.
I …
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I am following the Wiki to run: (see the screenshot attached)
All my bam and tsv files are generated correctly but when I am trying run the .sh file attached, I encountered a .slurm file and it…
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The tutorial mentions use of a RNA multiome file[(`reference = snap.read(snap.datasets.pbmc10k_multiome(), backed=None`)] for annotation of clusters in scATAC dataset (https://kzhang.org/SnapATAC2/tut…
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### Q2 Scope
Theme: Lay the groundwork for increasing the availability of analysis of new assays and species in the DCP.
Demo: Showing scATAC-seq pipeline in Job Manager.
ACs:
- Beta pipelines exist …
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Hi,
I want to preprocess some scATAC-seq datasets properly. I have seen episcanpy tutorials. I do binarization, variant peak selection and use `regress_out` method but still get poor results. Would…
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Hello,
I have been trying to use the mapping feature on two different scATAC-seq datasets. Both are able to infer trajectories individually. However, when trying to use the mapping feature (with …
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Dear all,
What is the corresponding table in case of mouse genome in this command?
genes.df = read.table("gencode.v19.annotation.gene.bed");
Thanks
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I went through both the vignettes that are available. However, I was wondering if there was more on how to generate the .rds files for scRNA (sparsematrix) and scATAC seq (SummarizedExperiment).
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I'm aligning 10x genomics scATAC-seq to the rheMac10 genome. The sequencing is 50bp for R1 and R2 paired-end sequencing on the Novaseq. The genome was built with k`17` and w`7` for min frag `30`. But …
badoi updated
2 years ago