Hi all,
I’m using Cell Ranger 9.0.0 to process some 5′ single-cell RNA-seq samples from NGS mice engrafted with human tumoral cells. The samples include gene expression, VDJ, and OligoHashtag libraries. I’m running cellranger multi with a combined reference (GRCh38 + GRCh38_two_transgenes + GRCm39) to try and detect the human transgenes in the cells.
In previous Cell Ranger versions (e.g., 7.x), I used to get a gem_classification.csv file under the analysis folder, which indicated whether a cell was of mouse or human origin. In Cell Ranger 9, this file no longer appears, and I can't find any clear equivalent. Here is a simplified version of my CSV config:
[gene-expression]
reference,/path/to/GRCh38_and_GRCm39_combined_reference
create-bam,false
force-cells,10000
tenx-cloud-token-path,/path/to/credentials
cell-annotation-model,auto
[feature]
reference,/path/to/barcode_sample_assignment.csv
[vdj]
reference,/path/to/vdj_reference
[libraries]
fastq_id,fastqs,lanes,feature_types
sample1,/path/to/GEX/fastqs,1|2,gene expression
sample1,/path/to/VDJ/fastqs,1|2,vdj
sample1,/path/to/Hashtags/fastqs,1|2,antibody capture
And and example of the barcode_sample_assignment.csv:
id,name,read,pattern,sequence,feature_type
Hash_1,Hash_2,R2,5PNNNNNNNNNN(BC),GTCAAAACCCCAGCG,Antibody Capture
...
Important: I’m not demultiplexing the hashtags at this stage — that step comes later. Question: Does Cell Ranger 9 no longer generate gem_classification.csv or any equivalent file indicating host species classification in multi-species references? Is there a new way to access this information, or am I missing a config option? Any help will be very appreciated!
Reach out to 10x tech support since you have not received a response yet. They should provide an official answer, in case this output file has been removed from v.9.x. Sometimes changes are made (this is a major version release) that are not reflected in the documentation right away.
Please post their response here, when you get one.
Thanks GenoMax I did that the next day I saw I didn't get the answer here, I am coming back now.
This is what 10x answered:
"Thank you for providing the information. We have not tested and do not support analysis of human + mouse samples with data modality besides GEX. It's likely that the gem_classification.csv file is not generated because there are data types in addition to GEX in the particular analysis."
You will need to drop the other assays besides GEX to get the that file then or find an alternate solution.