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I'm just following the tutorial for 10x multiome in the document. I have errors for ATAC-seq preprocessing.
I would like to ask all the errors that I encountered when I ran following function.
…
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Hi I am using RunChromVAR to compute motif activity on a scATAC-seq object of ~40k cells and 253k peaks.
It has not finished after running for nearly an hour. Is there any benchmarking or ETA for …
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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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**Describe the bug**
Here's a bug I encountered creating ArrowFiles, the following is my code :
```
library(ArchR)
addArchRGenome("hg38")
if (!requireNamespace("BiocManager", quietly = TRUE…
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I used my own scATAC-seq data from the mouse pbmc to calculate the cell age, and the count was based on mm10. But when it runs, it says
”**please make double sure your ref genome, peak set and cells…
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Hello :)
I first tried to use snapatac2 and snaptools to process scATAC-seq in whole mouse brain dataset.
Because I don't know well about snakemake pipeline, so I manually tried to process those d…
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Hello,
I have met the same issue as previously described by yejg2017. When I was trying to RunHarmony with my 10X-ATAC data (reduction = 'lsi'), harmony did not work well.
```
Harmony converge…
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Hello,
I generated a snap file from cellranger bam output. Then I used snapatac to cluster the cells. However, now when I try to run the runMACSForAll() function, I get the following errors. Is th…
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```
query= snap.pp.make_gene_matrix(atac, snap.genome.hg38)
query
AnnData object with n_obs × n_vars = 58534 × 60606
obs: 'sample', 'leiden'
reference=snap.read("GEX.h5ad", backed=None)
AnnD…
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I am trying to run ATACorrect for a bulk scATAC-seq BAM file, but I get.
[ERROR] No common contigs left to run ATACorrect on. Please check that '--bam' and '--fasta' are matching
The header of t…