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Dear muon-team,
I have converted my scATAC-seq SeuratObject to a mudata object but the information on the fragments files does not seem to be transferred. mdata.uns is empty.
My object is a merge…
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When run the tutorial in the document:
https://www.archrproject.com/bookdown/cross-platform-linkage-of-scatac-seq-cells-with-scrna-seq-cells.html
```{r}
projHeme2
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## **Describe the bug**
conda environment python2
## **OS/Platform**
- OS/Platform: local computer
- Conda version: 4.11.0
- Pipeline version: v2.0.3
- Caper version: v1.2.0
## **Caper co…
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I am trying to run the example JSON using singularity and the job keeps getting stuck without a clear error message. This is the command I'm running:
```
echo "source /broad/software/scripts/useus…
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Bulk ATAC-seq needs a new field for library adapters.
Two features:
1. The adapters should be per-library, so the field will be implemented as part of Library model.
2. submission code for Bulk A…
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ATAC-seq pipeline exit if no mitochondrial reads are duplicated due to zero division error - see logfile:
File "/Users/christianschmidl/src/open_pipelines/pipelines/atacseq.py", line 359, in parse_du…
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Hi!
I tried to make snap object from my own aligned BED file by snaptools 1.4.3.
snaptools snap-pre --input-file=snaptools_input_sorted.bed --output-snap=out.snap --genome-name=mm10 --genome-size=…
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I was wondering why the ChIP-Seq pipeline doesn't include an adapter trimming step like in the ATAC-Seq pipeline. Are adapter-trimmed FASTQs required for this pipeline?
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Thanks you for developing snapATAC tools,
and i have a question:
I followed the "Integrative Analysis of PBMC scATAC-seq and scRNA-seq" pipeline.
1. drawing the prediction score in histogram…
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https://github.com/haibol2016/ATACseqQCWorkshop