Deconvolution file corresponding to 1160920F Patient counts from the zenodo repository.

[ZheFrench]

For the patient 1160920F related to here https://zenodo.org/record/4739739#.Y007vNJBxhE, I would like to know which deconvolution ouput is corresponding in here : https://github.com/Swarbricklab-code/BrCa_cell_atlas/tree/main/spatial_analysis/stsc/major [182963_1160920F-count-matrix.tsv] [182968_1160920F-count-matrix.tsv] [182969_1160920F-count-matrix.tsv]

From the metadata, here. https://github.com/Swarbricklab-code/BrCa_cell_atlas/blob/main/spatial_analysis/Meta_Data.csv I bet it's 182968_1160920F. Right ? Thanks.

Update : Also the index given for the spots correspond to the merge of pxl_row_in_fullres X pxl_col_in_fullres. This is not array_row X array_col. Thanks

[johnyaku]

Yes, you are correct: the samples used in the paper are those listed in the meta data, namely:

• 182964_1142243F
• 182968_1160920F
• CID4290
• CID4465
• CID44971
• CID4535

I have removed the stereoscope results for the unused samples to avoid confusion. Thanks for bringing this to our attention.

And yes, the default spot indices used by Stereoscope are confusing. There is an option to preserve the barcode spot indices. Due to the ongoing interest in the results from this paper we are reworking this to include the Stereoscope processing, etc. We will look to simplify this in a later release.

[elliewith]

Where can I find the deconvolution results for: CID4290 CID4465 CID44971 CID4535

I can see the results for: 182964_1142243F 182968_1160920F