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Hi, I do know that this is far from ideal, but what's your opinion about the recommended parameters for single-end ATAC seq?
Thank you so much for your help!
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I'd like to call NFR only peaks for a pair-ended dataset. I'll try to limit the fragments to 150 bp. I could use "-I 150" option with Bowtie2, or filter the
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Dear Team,
The pipeline for ATAC Seq analysis, I and my team are working on need the R version 4.3 in RStudio in order to install and use all the required packages and dependencies.
I would lik…
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### Description of the bug
When running the atac-seq pipeline on our SLURM cluster, it keeps failing at seemingly arbitrary points, with an error message saying that the process was "terminated for a…
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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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**Describe the bug**
A clear and concise description of what the problem is.
**OS/Platform**
- OS/Platform: [e.g. Ubuntu 16.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
- Conda version:…
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Hi,
I'm trying to install Taiji from the source code in our CentOS server using stack and I'm getting requested to give my github credentials during the installation:
```
[gascui@login02 Taij…
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Exception thrown on pipeline launch, seems to be a Caper problem (get same output when running caper without input JSON). Running on SLURM cluster with pipeline v1.8.0.
**Caper configuration file**…
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## **Describe the bug**
I am trying to install the atac-seq-pipeline and having issues with installing the conda environments to even get the pipeline installed. Have been trying this for few weeks n…
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Hi @akundaje @leepc12 , I noticed that the README was updated like an hour ago, which basically says that the WDL-based pipeline is an exact copy of this pipeline. However, what I found was that using…