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Hello,
I have also been researching the GSE139136 scATAC-seq data recently. However, after downloading the files from SRA and running fastq-dump, I only obtained the paired-end sequencing files SRR…
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Hi !
I am trying tu use msCENTIPEDE to generate TF footprints for several ATAC-seq data sets i've produced.
I wanted to have general advices on how to achieve the most accurate workflow.
So far, w…
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Is it applicable for two samples to calculate the variability in normal ATAC-Seq but not single cell sequence?
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Dear developers,
I wonder if there is documentation/example for training based on Dnase/ATAC-seq input? I would highly appreciate suggestions on parameter tweaking!!
It seems ATAC/Dnase are supp…
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I am wondering if you have a step-by-step guide, clearly written to find ATAC-QTL? I find it difficult to use the tool to analyze based on the current documentation provided..
Thank you.
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### Name of the tool
ataqv
### Tool homepage
https://github.com/ParkerLab/ataqv/
### Tool description
ATAC-seq QC and visualization
### Tool output
```
% head GM12878_FAST_REP1.ata…
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Hi kai,
When using Taiji, I encountered some issues while using a YAML file as input. The error message I encountered is:
there is my input.yml:
```python
RNA-seq:
- id: RNA_NIP_0h
…
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The MC2 Center data model does not currently enable assay-specific metadata to be recorded. Adding these models is a critical part of supporting data sharing and reuse. Potential models to add were or…
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https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html
This is the single bad option. If fixed-up, tutorial's entire wf runs great at ORG :)
…
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Hi!
I was following the tutorial for integrating scRNA-seq data and scATAC-seq data using the dataset provided. However, I get the following error when I run the step: atac = tfl.findNeighbors(adat…