How to read in Primary Motor Cortex 10X-v3/v2 data into R/Seurat

Technical
1

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[[2]] (91072) is not equal to Dim[2] (91071)*

I tried various motor cortex 10x files and Dimnames[[2]] is always greater than Dim[2] 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

Thank you!
Gaurav

2

Hi Gaurav,

Thanks for your question, and glad to hear you are finding the Cell Type Knowledge Explorer and NeMO useful! These data should be readable using Seurat, and I think the error might be because the “barcode.tsv” file has a header row - if you remove that row, does the Read10X function work for you?

Thanks!
Ray

3

Yes that worked thank you!

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