Seurat: Read10X error: Barcode file missing

[thaocad]

Hi,
I would like to use Read10X on mouse bone marrow data available in https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128423

Yet I got this same error message: Error in Read10X(data_dir) : Barcode file missing

But when I checked, the barcode file was there:

list.files(data_dir)
[1] "GSM3674240_b2.barcodes.tsv" "GSM3674240_b2.genes.tsv"
[3] "GSM3674240_b2.matrix.mtx"

I also checked in the paper, they used "Cellranger toolkit (version 2.0.1, 10X Genomics)". Is it the source of this problem? What should I do to resolve this?

I tried Read10X() with both gzipped and unzipped files, both did not work with same error. FYI, I am using Seurat 3.0

Thanks!

[evolvedmicrobe]

Hi @thaocad,

The issue is that the Read10X data expects data files named as they are by the Cell Ranger pipeline (see: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/2.0/output/matrices for the documentation of the output files).

When they uploaded the files they changed the names, so you'll have to convert them back into their original form (e.g. remove GSM3674240_b2. from all the file names). From the documentation of the function, you can see that list.files(data_dir) # Should show barcodes.tsv, genes.tsv, and matrix.mtx, that is the files without the prefix name.

Cheers,
Nigel

[thaocad]

Hi @evolvedmicrobe,
Thank you very much for your prompt reply. It works!!
Best,
Thao

[VP0521]

Hi,
I am trying to load raw files using Read 10X command but it says the following error:
Expression matrix file missing. Expecting matrix.mtx

All the file prefixes I removed it and now has the names: barcodes.tsv, genes.tsv, and matrix.mtx

Please help me with this!

[bmanzato]

Hi @VP0521. Have you solved your issue?

[VP0521]

Yes, thanks for the response!

On Mon, Dec 14, 2020 at 4:56 AM bmanzato [e-mail] wrote:

Hi @VP0521 https://github.com/VP0521. Have you solved your issue?

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Vikrant Piprode, Ph.D
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[bmanzato]

Hi,
I was actually asking because I have the same issue with barcodes.tsv:

library(Seurat)
data_dir <-
"/Users/benedettamanzato/Desktop/smartseq/bus_output_11k_SMARTSEQ/10xread_data"
list.files(data_dir) # Should show barcodes.tsv, genes.tsv, and matrix.mtx
[1] "barcodes.tsv" "features.tsv" "matrix.mtx"
datamatrix <- Read10X(data.dir = data_dir , gene.column = 1)
Error in Read10X(data.dir = data_dir, gene.column = 1) :
Barcode file missing. Expecting barcodes.tsv.gz

Do you remember how you solved it?

Best,
Benedetta

On Mon, Dec 14, 2020 at 11:54 AM VP0521 [e-mail] wrote:

Yes, thanks for the response!

On Mon, Dec 14, 2020 at 4:56 AM bmanzato [e-mail] wrote:

Hi @VP0521 https://github.com/VP0521. Have you solved your issue?

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Vikrant Piprode, Ph.D
Phone: [phone]

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[VP0521]

Hi,
You have to give correct directory to your command:
After you install seurat, pathwork and dplyr

use this commant
sample.data <- Read10X(data.dir = "/file location")

Note: Be careful with the caps and small alphabets also. They all should
match your file directory.

BEST

Vikrant Piprode, Ph.D
Phone: [phone]

On Mon, Dec 14, 2020 at 6:04 AM bmanzato [e-mail] wrote:

Hi,
I was actually asking because I have the same issue with barcodes.tsv:

library(Seurat)
data_dir <-

"/Users/benedettamanzato/Desktop/smartseq/bus_output_11k_SMARTSEQ/10xread_data"

list.files(data_dir) # Should show barcodes.tsv, genes.tsv, and
matrix.mtx
[1] "barcodes.tsv" "features.tsv" "matrix.mtx"
datamatrix <- Read10X(data.dir = data_dir , gene.column = 1)
Error in Read10X(data.dir = data_dir, gene.column = 1) :
Barcode file missing. Expecting barcodes.tsv.gz

Do you remember how you solved it?

Best,
Benedetta

On Mon, Dec 14, 2020 at 11:54 AM VP0521 [e-mail] wrote:

Yes, thanks for the response!

On Mon, Dec 14, 2020 at 4:56 AM bmanzato [e-mail]
wrote:

Hi @VP0521 https://github.com/VP0521. Have you solved your issue?

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Vikrant Piprode, Ph.D
Phone: [phone]

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[bmanzato]

Hi,

thank you for your response. Actually I already solved that problem.

Now I have a new one and don't really know how to solve it:

datamatrix <- Read10X(data.dir = data_dir , gene.column = 1,
unique.features = TRUE)
Error in dimnamesGets(x, value) :
invalid dimnames given for “dgTMatrix” object

Has this happened to you too?

On Mon, Dec 14, 2020 at 5:53 PM VP0521 [e-mail] wrote:

Hi,
You have to give correct directory to your command:
After you install seurat, pathwork and dplyr

use this commant
sample.data <- Read10X(data.dir = "/file location")

Note: Be careful with the caps and small alphabets also. They all should
match your file directory.

BEST

Vikrant Piprode, Ph.D
Phone: [phone]

On Mon, Dec 14, 2020 at 6:04 AM bmanzato [e-mail] wrote:

Hi,
I was actually asking because I have the same issue with barcodes.tsv:

library(Seurat)
data_dir <-

"/Users/benedettamanzato/Desktop/smartseq/bus_output_11k_SMARTSEQ/10xread_data"

list.files(data_dir) # Should show barcodes.tsv, genes.tsv, and
matrix.mtx
[1] "barcodes.tsv" "features.tsv" "matrix.mtx"
datamatrix <- Read10X(data.dir = data_dir , gene.column = 1)
Error in Read10X(data.dir = data_dir, gene.column = 1) :
Barcode file missing. Expecting barcodes.tsv.gz

Do you remember how you solved it?

Best,
Benedetta

On Mon, Dec 14, 2020 at 11:54 AM VP0521 [e-mail]
wrote:

Yes, thanks for the response!

On Mon, Dec 14, 2020 at 4:56 AM bmanzato [e-mail]
wrote:

Hi @VP0521 https://github.com/VP0521. Have you solved your issue?

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You are receiving this because you were mentioned.
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Vikrant Piprode, Ph.D
Phone: [phone]

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