Hi thank you so much for the incredible resource ‘Cell Type Knowledge Explorer’ with links to download the 10x v3/v2 data.
I was wondering if there were any guides to reading this data into R so it can be used with Seurat?
I have tried the following:
-Download the matrix.tsv.gz, features.tsv.gz and barcode.tsv
-Rename barcode.tsv to barcodes.tsv.gz
-Run Read10X command in R
(This strategy has worked for me on some of the human 10x transcriptomic data shared on NeMO)
However, with the motor cortex data, when I try the ‘Read10X’ command in R/Seurat, I get the following error:
*Error in dimnamesGets(x, value) : *
- length of Dimnames[] (91072) is not equal to Dim (91071)*
I tried various motor cortex 10x files and Dimnames[] is always greater than Dim by just 1
If this data is not readable with Seurat, would someone kindly point me towards how I can best read in this data with Python?
At the end of the day, I’m basically just trying to recreate Gene Expression by Cluster, median and Gene Expression by Cluster, trimmed means as is shared for the Mouse Whole Cortex / Hippocampus, except I would love such files for the Mouse Primary Motor Cortex only