# How to make the union set of 2 scRNA-seq matrix?

**URL:** <https://discourse.scverse.org/t/how-to-make-the-union-set-of-2-scrna-seq-matrix/452>\
**Category:** anndata\
**Created:** [May 13, 2022, 8:05pm UTC](https://discourse.scverse.org/t/how-to-make-the-union-set-of-2-scrna-seq-matrix/452 "2022-05-13T20:05:50Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![hyjforesight](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/hyjforesight/32/229_2.png) [@hyjforesight](https://discourse.scverse.org/u/hyjforesight)\
**Post date:** [May 13, 2022, 8:05pm UTC](https://discourse.scverse.org/t/how-to-make-the-union-set-of-2-scrna-seq-matrix/452/1 "2022-05-13T20:05:50Z")

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Hello Scanpy,  
We have 2 scRNA-seq libraries sharing some common barcodes between them. We want to make a union set of these 2 libraries by removing the duplicated barcodes? But we’re not professional with the anndata coding. It looks like we cannot do it by simple | or & or - or ^ in pandas.  
Could you please help us with this question?  
Thanks!  
Best,  
YJ

We tried:

```python
CKP1 = sc.read_10x_mtx(path='D:/ZGY/MST_matrix/KP9CKP11-5_11/CKP/', var_names='gene_symbols', cache=True) 
CKP1.var_names_make_unique()
CKP2 = sc.read_10x_mtx(path='D:/ZGY/MST_matrix/KP10CKP12-5_11/CKP/', var_names='gene_symbols', cache=True)
CKP2.var_names_make_unique()

dup_index = CKP1.obs_names.intersection(CKP2.obs_names) # find the duplicated index between 2 libraries
dup_index
Index(['AAACCCACACCTTCGT-1', 'AAACCCACACTACAGT-1', 'AAACCCACAGATACCT-1',
       'AAACCCACAGCGTTTA-1', 'AAACCCACAGGCCTGT-1', 'AAACCCACATGAGATA-1',
       'AAACCCAGTAATCAAG-1', 'AAACCCAGTCGCCTAG-1', 'AAACCCAGTGTCATCA-1',
       'AAACCCAGTGTCCATA-1',
       ...
       'TTTGTTGCATAGAGGC-1', 'TTTGTTGCATGAGATA-1', 'TTTGTTGGTCGTACTA-1',
       'TTTGTTGGTGCGGCTT-1', 'TTTGTTGGTTGTGTTG-1', 'TTTGTTGTCAAAGCCT-1',
       'TTTGTTGTCACCCTTG-1', 'TTTGTTGTCCTCGCAT-1', 'TTTGTTGTCGCTTAAG-1',
       'TTTGTTGTCTCGCAGG-1'],
      dtype='object', length=9697)

CKP1_uni=CKP1-CKP1[dup_index,:] # slice the unique part of CKP1
TypeError: unsupported operand type(s) for -: 'AnnData' and 'AnnData'
CKP2_uni=CKP2-CKP2[dup_index,:] # slice the unique part of CKP2
TypeError: unsupported operand type(s) for -: 'AnnData' and 'AnnData'
CKP_intersection=CKP1[dup_index,:] # slice the intersection part of CKP1 and CKP2
View of AnnData object with n_obs × n_vars = 9697 × 32285
    var: 'gene_ids', 'feature_types'

adata = CKP1_uni.concatenate(CKP2_uni, CKP_intersection, batch_categories=['CKP1_uni', 'CKP2_uni', 'CKP_intersection']) # merge these 3 parts
NameError: name 'CKP1_uni' is not defined

```

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<div class="post-metadata">

**Author:** ![Valentine\_Svensson](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/valentine_svensson/32/10_2.png) [@Valentine\_Svensson](https://discourse.scverse.org/u/Valentine_Svensson)\
**Post date:** [May 15, 2022, 10:41pm UTC](https://discourse.scverse.org/t/how-to-make-the-union-set-of-2-scrna-seq-matrix/452/2 "2022-05-15T22:41:00Z")

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Hi YJ,

Index objects acts as `set`s. You have gotten pretty far to how I would solve this with the first bit. Here’s what I would do:

```auto
idx1 = CKP1.obs.index
idx2 = CKP2.obs.index
dup_index = idx1.intersection(idx2)
unique_idx1 = idx1.difference(dup_index)
unique_idx2 = idx2.difference(dup_index)

CKP1_uni = CKP1[unique_idx1, :].copy()
CKP2_uni = CKP2[unique_idx2, :].copy()
CKP_intersection = CKP1[dup_index, :].copy()

adata = anndata.concatenate((CKP1_uni, CKP2_uni, CKP_intersection))

```

The error you are seeing (`TypeError: unsupported operand type(s) for -: 'AnnData' and 'AnnData'`) is because it hasn’t been defined what `adata1 - adata2` means. So instead I am creating unique indices and intersection of the indices, then slice by those.

Now, I am not sure what this data is. But if you have two sequenced librariries of the same samples, I would probably add up the molecule counts from both ` CKP1[dup_index, :]` and ` CKP2[dup_index, :]`. Though it’s hard to know if the UMIs are unique between them.

Hope this helps!  
/Valentine

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<div class="post-metadata">

**Author:** ![hyjforesight](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/hyjforesight/32/229_2.png) [@hyjforesight](https://discourse.scverse.org/u/hyjforesight)\
**Post date:** [May 16, 2022, 12:02am UTC](https://discourse.scverse.org/t/how-to-make-the-union-set-of-2-scrna-seq-matrix/452/3 "2022-05-16T00:02:23Z")

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Hello Valentine,  
Thanks for the solution! Appreciate it! You saved our data!  
We’ll revisit this post once we publish our data and make the acknowledgment for you!  
Thanks!  
Best,  
YJ