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Dear Author,
Thank you for developing such a perfect model like C.Origami. It's a great work, but I have encountered some difficulties.
First, I have DNA sequence information from other species,…
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scEmbed is an excellent job that provides an dimensionality reduction encoding for scATAC-seq data. When I tried to use it to map my data, I found that it took an extremely long time to run model.enco…
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QC pipeline ran to completion with two samples called "IRI" and "Sham". Trying DAR with following command.
`singularity exec /home/[my-path]/ATAC_IAP_v1.1.simg bash /atac_seq/pipe_code/DOR_anal…
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Hi, thanks for this nice tool!
I wanted to understand the usage of CORE-ATAC conceptually. So, for creating training-set peaks, we will need peaks regions identified from bulk-ATAC-seq? I have scATAC…
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Hi!
Any advice for running deepvariant on single-cell ATAC-seq data? I assumed RNA-seq would be most similar but that is still quite different.
Thanks!
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Add library complexity metrics from Encode: Non-redundant fraction (NRF) and PCR bottleneck coefficients 1 and 2 (PCB1 and PCB2). Example code can be seen in Yiewei Niu's [ATAC-seq data analysis: from…
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Hi,
We have a ATAC/RNA-seq pair-end reads for the input. What kind of options should we be using for the mapping part? What should we expect for the output?
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I have four different 10x multiome seurat object (one for each experiment). I am able to integrate the RNA assay without much issue.
```r
merge_obj
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Usually it is paired-ends 50bp reads for ATAC-seq. Can this pipeline be used for analyzing paired-end 75bp reads?
Thanks!
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Hi developers,
Nice method and code/documentation! I was wondering how feasible is to apply ANANSE to single-cell multiomics data (RNA+ATAC):
- For scalability, should I pseudobulk cells by cell…