Loading 10X V(D)J data

[barakt123]

Hey, I am using cellranger version 7.0 and running the cellranger vdj function. The output of cellranger vdj function contains a folder named outs (as described here https://support.10xgenomics.com/single-cell-vdj/software/pipelines/7.0/tutorial/tutorial-vdj). I am trying to load the data using repLoad (The path I gave to the function is to the outs folder) and get the following error: Error in if (str_detect(l, "CDR3 amino acid sequence") && str_detect(l, : missing value where TRUE/FALSE needed Would appreciate any help.. Thanks :)

[Alexander230]

Hi, @barakt123!

I'm Aleksandr, a developer of Immunarch package. Thank you for using our software!

Looks like some files in this folder contain empty files or unsupported by Immunarch. Also, it's possible that the version of installed Immunarch is outdated. I've made an experimental fix for wrong empty files handling (which seems to be the cause of this error message). Please install the fixed version and check what will happen if you try to load these files. You can also try to load individual files from the folder.

To install the fixed version, use the following commands:

install.packages(c("devtools", "pkgload"))
devtools::install_github("immunomind/immunarch", ref="better-empty-file-handling")
devtools::reload(pkgload::inst("immunarch"))

When the fix will be finalized, it will be moved to dev branch; after that, to install it, use ref="dev" instead of ref="better-empty-file-handling" in these commands.

Best regards, Aleksandr

[barakt123]

Hi Aleksandr, Thank you for your quick response!

I'm still having trouble with loading my data. I have 12 samples (12 outputs from cell ranger vdj). There is “outs” folder for each sample, which contains the following:

[cid:94847D10-4C65-4918-83B3-C981EF0EC3A6]

I have tried to use the code that you sent me:

install.packages(c("devtools", "pkgload")) devtools::install_github("immunomind/immunarch", ref="better-empty-file-handling") devtools::reload(pkgload::inst("immunarch"))

But I still having some issues..

I'm working on R 4.1.1 and use cellranger 7.0

In addition, I have another question: How can I merge / integrate my 12 samples (like merging Seurat objects)? Thank you for your time, Barak :)

WIS Barak @.**@.>

On 25 May 2022, at 1:34, Aleksandr Popov @.**@.>> wrote:

Hi, @barakt123https://github.com/barakt123!

I'm Aleksandr, a developer of Immunarch package. Thank you for using our software!

Looks like some files in this folder contain empty files or unsupported by Immunarch. Also, it's possible that the version of installed Immunarch is outdated. I've made an experimental fix for wrong empty files handling (which seems to be the cause of this error message). Please install the fixed version and check what will happen if you try to load these files. You can also try to load individual files from the folder.

To install the fixed version, use the following commands:

install.packages(c("devtools", "pkgload")) devtools::install_github("immunomind/immunarch", ref="better-empty-file-handling") devtools::reload(pkgload::inst("immunarch"))

When the fix will be finalized, it will be moved to dev branch; after that, to install it, use ref="dev" instead of ref="better-empty-file-handling" in these commands.

Best regards, Aleksandr

— Reply to this email directly, view it on GitHubhttps://github.com/immunomind/immunarch/issues/240#issuecomment-1136493331, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZJI2RHJALVUFZEITGJZDZLVLVKQTANCNFSM5WVW2DEQ. You are receiving this because you were mentioned.Message ID: @.***>