cellRanger 2.0 to Seurat 3.1.2

Question

[cge]

Hi, anybody know if data from cellRanger 2.0 are still readable with Seurat 3.1.2? I am getting an error, I saw several threads but still no luck. Thanks S.

[ATpoint]

Yes, it is. Please add details. "I am getting an error" is not a reproducible error description. Show code and exact error messages please.

[cge]

Hi, thank you for you answer. Here the code and error:

mat <- Read10X(data.dir = dataDir)
Error in dimnamesGets(x, value) :  
 invalid dimnames given for “dgTMatrix” object
In addition: Warning messages: 1: In readLines(barcode.loc) : line 15647540 appears to contain an embedded nul
2: In readLines(barcode.loc) : incomplete final line found on '/data/barcodes.tsv'

Answer 1

[igor]

As the error says, you have an incomplete line. That probably means that there was an error in transferring the file.

Answer 2

[cge]

Thanks! I downloaded again the file and it worked. S.