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Thank you very much for developing the excellent ATAC-seq package.
I'm encountering an issue with the part “the function loads the pre-computed bias in the regions of interest”. I'm following your tu…
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I have installed snakepipes and downloaded ATACseq example for test run. However, the example does not run as I expected.
I first run following the suggestion from command.sh and get this:
#####
(s…
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Hello,
After running your software, I noticed that some beads were classified as originating from the same cell. Could you please explain how this determination is made? Specifically, I'm curious a…
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Hi there,
I have a problem running the pipeline which I have set up on a SLURM HPC. It had worked previously and I used it regularly for the best part of a year. However it stopped working after a …
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## **Describe the bug**
When running the pipeline, the number of reads in the "Fraction of mitochondrial reads" table does not match the number of reads in some of the other tables. For example, on …
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Can this platform be used for shallow scATAC-seq data? I have output from cellranger atac count pipeline. How can I generate doubletD inputs from this?
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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/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/runMACS.R#L32
According to the [MACS2 page](https://github.com/taoliu/MACS) the settings
```--shift -100 --extsi…
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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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## **Describe the bug**
Hi team,
I tried to peak-call using input files as dedupped BAM files. It worked initially for 1 sample (2 replicates), but not for the second sample.
## **OS/Platform**…