Important
T cell libraries enriched for gamma (TRG) and delta (TRD) chains can only be analyzed using Cell Ranger v7.0.0 and later.
Here are some example multi config CSVs to be used as inputs for running cellranger multi on T cell libraries enriched for gamma (TRG) and delta (TRD) chains. Make sure to replace /path/to with the actual full path to your data, and edit any text in red according to the experiment's sample/library/file names.
[vdj]
reference,/path/to/vdj_reference
inner-enrichment-primers,/path/to/primers.txt
[libraries]
fastq_id,fastqs,lanes,feature_types,subsample_rate
VDJ_GD_fastqs_id,/path/to/vdj_GD_fastqs,1|2,VDJ-T-GD,
[gene-expression]
reference,/path/to/transcriptome
[vdj]
reference,/path/to/vdj_reference
inner-enrichment-primers,/path/to/primers.txt
[libraries]
fastq_id,fastqs,lanes,feature_types,subsample_rate
GEX_fastqs_id,/path/to/GEX_fastqs,1|2,Gene Expression,
VDJ_GD_fastqs_id,/path/to/vdj_GD_fastqs,1|2,VDJ-T-GD,
[gene-expression]
reference,/path/to/transcriptome
[vdj]
reference,/path/to/vdj_reference
inner-enrichment-primers,/path/to/primers.txt
[feature]
reference,/path/to/feature_ref.csv
[libraries]
fastq_id,fastqs,lanes,feature_types,subsample_rate
VDJ_B_fastqs_id,/path/to/vdj_B_fastqs,1|2,VDJ-B,
VDJ_T_GD_fastqs_id,/path/to/vdj_T_GD_fastqs,1|2,VDJ-T-GD,
FB_fastqs_id,/path/to/FB_fastqs,1|2,Antibody Capture,
This template is similar to GEX + V(D)J + FB libraries. The [gene-expression] reference section is required. However, the GEX FASTQ specification under the [libraries] section must not be present for the VDJ+FB library combinations.
[gene-expression]
reference,/path/to/transcriptome
[vdj]
reference,/path/to/vdj_reference
inner-enrichment-primers,/path/to/primers.txt
[feature]
reference,/path/to/feature_ref.csv
[libraries]
fastq_id,fastqs,lanes,feature_types,subsample_rate
GEX_fastqs_id, /path/to/GEX_fastqs,1|2,Gene Expression,
FB_AB_fastqs_id, /path/to/FB_fastqs,1|2,Antibody Capture,
FB_CRISPR_fastqs_id, /path/to/CRISPR_fastqs,1|2,CRISPR Guide Capture,
VDJ_B_fastqs_id, /path/to/vdj_B_fastqs,1|2,VDJ-B,
VDJ_T_fastqs_id, /path/to/vdj_T_fastqs,1|2,VDJ-T,
VDJ_T_GD_fastqs_id, /path/to/vdj_T_GD_fastqs,1|2,VDJ-T-GD,