# Counts in layers is zero after ad.concat

**URL:** <https://discourse.scverse.org/t/counts-in-layers-is-zero-after-ad-concat/1999>\
**Category:** anndata\
**Created:** [January 13, 2024, 5:26am UTC](https://discourse.scverse.org/t/counts-in-layers-is-zero-after-ad-concat/1999 "2024-01-13T05:26:05Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![malonzm1](https://avatars.discourse-cdn.com/v4/letter/m/9de0a6/32.png) [@malonzm1](https://discourse.scverse.org/u/malonzm1)\
**Post date:** [January 13, 2024, 5:26am UTC](https://discourse.scverse.org/t/counts-in-layers-is-zero-after-ad-concat/1999/1 "2024-01-13T05:26:05Z")

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Hi,

I filter each dataset before ad.concat:

```auto
sc.pp.filter_genes(adata, min_cells = 3)
sc.pp.filter_cells(adata, min_genes = 200)
sc.pp.filter_cells(adata, min_counts = 200)

```

I also tried

```auto
sc.pp.filter_cells(adata, min_counts = 200)
sc.pp.filter_genes(adata, min_counts=3)
sc.pp.filter_genes(adata, min_cells = 3)

```

Then

`ad.experimental.concat_on_disk(in_files = infiles, merge = 'same', out_file = '10x_all.h5ad')`

But some of the sub datasets return zero counts in layers. Why do I get zero counts when I’ve already filtered the sub datasets to have \>= 200 genes? Any help would be much appreciated.

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<div class="post-metadata">

**Author:** ![malonzm1](https://avatars.discourse-cdn.com/v4/letter/m/9de0a6/32.png) [@malonzm1](https://discourse.scverse.org/u/malonzm1)\
**Post date:** [January 15, 2024, 4:26am UTC](https://discourse.scverse.org/t/counts-in-layers-is-zero-after-ad-concat/1999/2 "2024-01-15T04:26:18Z")

</div>

I figured out that using ad.experimental.concat\_on\_disk caused the zero counts. Reverting to ad.concat solved the problem.

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<div class="post-metadata">

**Author:** ![ivirshup](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/ivirshup/32/160_2.png) [@ivirshup](https://discourse.scverse.org/u/ivirshup)\
**Post date:** [January 15, 2024, 9:45am UTC](https://discourse.scverse.org/t/counts-in-layers-is-zero-after-ad-concat/1999/3 "2024-01-15T09:45:33Z")

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Could you open an issue on `anndata` for this? It seems like a bug in `concat_on_disk`