CITEsq loading in RNA and ADT data

Help scanpy
1

Hello everyone,

I’m in to process of learning single cell analysis. Thus far I’ve within my first week made good progress in analysing single cell data by using Scanpy.

However I’ve hade som trouble analysing a publicly available CITE-seq dataset. My problem is very basic, the data is uploaded in this manner:

ADT_barcodes.tsv.gz|
ADT_counts.txt.gz
ADT_tags.tsv.gz|
barcodes.tsv.gz|
features.tsv.gz|
hashtags.csv.gz|
matrix.mtx.gz|

I’ve only found tutorials showing how to load h5.files containing the above, but I’ve had a hard time figuring out how to create an AnnData containing all of the above.

I would be very happy for any of your suggestions.

2

I just realized I made a post with a very similar problem as yours. Did you figure out a solution?

3

Sorry, for late response. yet to find a solution, haven’t had time to work on it since my last message. Please update me if you’ve found a way.

4
5

Basically you have a multiomics experiment so why not use MuData and muon for this? You can try:

import muon as mu

mdata = mu.MuData({
  "rna": adata_gex,
  "prot": adata_adt
})

(Of course, use any names you like in place of “rna” and “prot” in the dict).

It is possible that you do not even need to subset the objects with the intersection of barcodes but depending on your specific problem that might be what you want to do anyway.

You can check the muon website on how to use them:

Muon

And the muon/mdata categories in this site for more specific help on those tools.

Hope this helps!

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