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Hi,
Thanks for developing such an excellent tool for single-cell genomics. I am wondering whether you could provide the processing pipeline for Easysci-ATAC-seq.
Thanks.
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Hi,
I understand that the default mapping option for the ATAC-seq data is pair ended, but is there a mapping option for a single ended ATAC-seq data?
Thank you,
Lindsay
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Hello,
I was wondering if TEpeaks would work for ATAC-seq peaks? Have you ever tried it?
Thank you
Rita
RRebo updated
3 months ago
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Hello,
I'm interested in using scglue to integrate my scRNAseq with scATACseq data, comprising four paired samples. These datasets are not multiome; they're only paired samples.
After processing…
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Hi!
I was following the tutorial for integrating scRNA-seq data and scATAC-seq data using the dataset provided. However, I get the following error when I run the step: atac = tfl.findNeighbors(adat…
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Hi,
Thanks for this pipeline.
I was trying to use it on atac-seq data. I got the following error message:
`Caused by: Process bamCoverage (1) terminated with an error exit status (127) Comma…
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https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html
This is the single bad option. If fixed-up, tutorial's entire wf runs great at ORG :)
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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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Dear,
Is it possible to use EPIC for cell type deconvolution using ATAC-seq datasets?
It gives the following error when I provide bulk ATAC-seq matrix (rows=peaks, columns=sample/subject) as inp…
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I am trying to call peaks in ATAC-seq data. According to the documentation:
> To find enriched cutting sites such as some DNAse-Seq datasets. In this case, all 5' ends of sequenced reads should be ex…