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Hello,
I am having issues running TOBIAS BINDetect. I get the following error --
Traceback (most recent call last):
File "/mnt/NewHDD/anaconda3/bin/TOBIAS", line 8, in
sys.exit(main())…
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I integrated two datasets with Harmony, and when I try to do atac-seq + scRNAseq alignment I get the following error at the anchoring step.
`rna_seurat`
An object of class Seurat
58361 features …
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Hi,
Is it possible to run integrated analysis similar to https://satijalab.org/seurat/v3.0/immune_alignment.html on scATAC seq data? Please see my attempt below with the error produced. I followed …
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Very useful tool and nice work out of Cell Systems!
Can DoubletFinder also be applied to scATAC-seq data?
One could perform PCA on the gene activity matrix:
DefaultAssay(pbmc.atac)
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@timoast Thank you for your reply. I have some followup questions. (with reference to #197)
> I would first quantify the same set of peaks for _all_ samples, following the workflow shown in the [me…
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Thanks a lot for developing this package. My scATAC-seq data was aligned to GRCh38. In your package, the human hg19 coordinates can be accessed with data("human.hg19.genome"). Where can I find the gen…
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Hi Tim,
Thanks for your excellent program for scATAC-seq analysis. Here I have a question about the motif analysis with Signac. I focus on cattle and there are 4 samples total. Below is the full code…
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http://epigenomics.sdsc.edu:8000/setqc/JYH_813/web_summary.html
may be other 10xATAC?
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Hi,
I am following the seurat vignette (https://satijalab.org/signac/articles/pbmc_vignette.html)
At the following stage, when loading the scRNA PBMC data R aborts.
```{r Load the pre-proces…
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I'm running the most recent commit on the master branch : 2020-07-13 ddcaae4 in R `3.6.3`
**Attach your log file**
[ArchR-createArrows-88a26534811-Date-2020-08-24_Time-14-02-14.log](https://github…