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Hello, I am running chromap to process scATAC-seq from 10x chromium as follows:
```
GENOME_FASTA="(...)/refdata-gex-GRCh38-2020-A/fasta/genome.fa"
GENOME_INDEX="(...)/refdata-gex-GRCh38-2020-A/fa…
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Thank you for this awesome repo. I want to train a model with multiple scATAC datasets. But I found they typically have different dimensions (different number of peaks). How should I deal with it? Is …
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Dear Charles,
Thanks for offering the awesome dataset and code.
I have downloaded the metadata and processed snRNA-seq (.h5ad) through the google bucket [here](https://console.cloud.google.com/s…
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**Describe the bug**
To reproduce
1. Have Python 3.9.15
2. Build scenicplus from source
3. Install fails at `fa2` dependency due to https://github.com/bhargavchippada/forceatlas2/issues/34
Work…
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Hello, I'm trying Genrich to call peaks for ATAC-seq data.
When doing motif finding and peak annotation, the peak summit file is needed, so I'm wonder how may I get the peak summit information from G…
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Hi,
I got the error when I apply the write_matrix_dir function. I have tried to re-install the BPCells, but still got this problem. Any suggestion? Thanks!
```
> write_matrix_dir(dat, "tmp")
W…
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When running gimme maelstrom (on a fresh gimme install), it will crash due to missing xgboost:
```
2022-11-29 11:54:29,527 - INFO - Starting maelstrom
2022-11-29 11:54:29,797 - INFO - Input is no…
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Hi everyone,
I run into an error during the ATAC-seq pipeline.
```
/home/jrummel/anaconda3/envs/snakePipes/bin/ATAC-seq -d /projects/allelespecificchromatinmouse/work/MouseSeqData/results/DNA…
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[ArchR-createArrows-4a21a718c956-Date-2023-03-02_Time-20-59-19.log](https://github.com/GreenleafLab/ArchR/files/10872161/ArchR-createArrows-4a21a718c956-Date-2023-03-02_Time-20-59-19.log)
When …
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https://mp.weixin.qq.com/s/zj9qeZah50ZWLa0GbUCMpw