# scATAC-seq

**URL:** https://discourse.scverse.org/c/general/scatac-seq/29.md

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## [About the scATAC-seq category](https://discourse.scverse.org/t/about-the-scatac-seq-category/322)

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**Author:** [@adamgayoso](https://discourse.scverse.org/u/adamgayoso)\
**Replies:** 0

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## [Normalizing scATACseq data](https://discourse.scverse.org/t/normalizing-scatacseq-data/2231)

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**Author:** [@philmar1](https://discourse.scverse.org/u/philmar1)\
**Replies:** 1\
**Last updated:** [April 23, 2024, 10:34pm UTC](https://discourse.scverse.org/t/normalizing-scatacseq-data/2231 "2024-04-23T22:34:56Z")

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Hello, I am opening a discussion on good practices to deal with scATACseq data. Can anyone please tell me: Whether or not you use binary count matrix as input to any model (PeakVI or other) How do you subset your tile…

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## [Visualisation of ATAC seq data in Python](https://discourse.scverse.org/t/visualisation-of-atac-seq-data-in-python/1909)

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**Author:** [@pouria](https://discourse.scverse.org/u/pouria)\
**Replies:** 0\
**Last updated:** [November 21, 2023, 3:15pm UTC](https://discourse.scverse.org/t/visualisation-of-atac-seq-data-in-python/1909 "2023-11-21T15:15:31Z")

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Hello Guys, I’ve just started analysing my first sc ATAC seq dataset. I’m using snapATAC2 and so far I’ve been able to preprocess, batchcorrect and cluster without any major problems. I’am however having problems crea…

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## [Converting h5 to h5ad files?](https://discourse.scverse.org/t/converting-h5-to-h5ad-files/527)

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**Author:** [@AdamT555](https://discourse.scverse.org/u/AdamT555)\
**Replies:** 2\
**Last updated:** [September 29, 2022, 7:03pm UTC](https://discourse.scverse.org/t/converting-h5-to-h5ad-files/527 "2022-09-29T19:03:26Z")

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Hi all, It seems like ScanPy and EpiScanPy like being fed h5ad files. Is there an easy way to convert from h5 to h5ad? Thanks in advance!

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## [Question about the markergene score](https://discourse.scverse.org/t/question-about-the-markergene-score/633)

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**Author:** [@yingyuan830](https://discourse.scverse.org/u/yingyuan830)\
**Replies:** 0\
**Last updated:** [July 20, 2022, 7:13pm UTC](https://discourse.scverse.org/t/question-about-the-markergene-score/633 "2022-07-20T19:13:06Z")

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When I used the function to plot markergene score, I am really confused whether the score of one specific marker gene is normalized ? If I’d like to compare the score of different marker gene for one cluster, should I do…

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## [Data preprocessing for scATAC-seq](https://discourse.scverse.org/t/data-preprocessing-for-scatac-seq/178)

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**Author:** [@tu.le](https://discourse.scverse.org/u/tu.le)\
**Replies:** 4\
**Last updated:** [September 10, 2021, 9:03pm UTC](https://discourse.scverse.org/t/data-preprocessing-for-scatac-seq/178 "2021-09-10T21:03:29Z")

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Hi Adam @adamgayoso, I would like to ask if scvi-tools supports functions for preprocessing scATAC-seq data, similar to what have been provided by Seurat, or not. For example, does it have function for filtering out cel…