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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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Hello,
I'm a research fellow at JHU.
I faced this problem when I tried the installation of the ataqv package.
Any suggestions?
~ $ brew install ataqv
==> Installing ataqv from parkerlab/tap
…
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Hello! I have installed the tool and called it (it states that there are 32 warnings) However, it seems to be loaded just fine. when I run it on the sample, the first part is done and the .rds file is…
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## **Invalid MEMLIMIT value with LSF on Linux**
When running the tutorial example for HPC with LSF, caper submits invalid memory unit format. Is lower case 'g' but should be 'G', resulting in the f…
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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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**Describe the bug**
Hi there,
I‘m using ArchR to analysis my ATAC data. And I want to do barcode filtering in `createArrowFiles` step. I found that `getValidBarcodes` could help me extract the val…
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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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Hi,
I have seen most papers doing ATAC-Seq analysis run macs2 with the --nolambda option, including the hmmratac paper. Naively, it seems like this would overcall peaks/peak summits in generally op…
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I am facing following error while using macs14
**Command used** : macs14 -t test.bam -c control.bam
**Error**
# ARGUMENTS LIST:
# name = NA
# format = AUTO
# ChIP-seq file =text4.bam
# control file =…
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# 1. 可能是 ATAC-seq 方法的原始文献 (nature methods, 2023)
https://www.nature.com/articles/nmeth.2688
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-bi…