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in functional-annotation/Rules/CallPeaks.smk, line 180,
No -B option used in macs2 callpeak command, which resulted in no treat_pileup.bdg files.
Then in rule fold_enrichment (line 199):
pip…
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I was recently working on ATAC data. Therefore, i wanted to ask if demuxalot can be used for ATAC data?
Because each time i try to use it for my data i get the following error.
**KeyError: “tag ‘N…
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Hi,
I have a question of using scGPT on ATAC data. The typical scATAC-seq has binarized values 0 and 1, so how to make the ATAC counts as bins? Should we only make the counts to only 2 bins: 0-bin an…
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T cell subsets are likely best distinguished w/ ATAC-seq data so we should track down some.
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Hi,
I've established a link to the FTS API interface and I can insert (POST) entities and then use ManageGeoObject/getGeoObject to retrieve them from the server. Also, when I add them using the API I…
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"I encountered this error while performing the analysis, how should I troubleshoot it?
```
Traceback (most recent call last):
File "/home/yanghj/miniconda3/lib/python3.9/multiprocessing/pool.py",…
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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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Hi,
when I tried to run caper with encode-atac-pipeline, I could see the job was submitted to the lsf system, but the job disappear immediately without any reports.
when I looked into the detai…