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 customize text according to the experiment's sample/library/file names.

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[vdj]
reference,/path/to/vdj_reference
inner-enrichment-primers,/path/to/primers.txt

[libraries]
fastq_id,fastqs,lanes,feature_types,
VDJ_GD_fastqs_id,/path/to/vdj_GD_fastqs,1|2,VDJ-T-GD,

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[gene-expression]
reference,/path/to/transcriptome
create-bam,true

[vdj]
reference,/path/to/vdj_reference
inner-enrichment-primers,/path/to/primers.txt

[libraries]
fastq_id,fastqs,lanes,feature_types,
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,

Copy
[gene-expression]
reference,/path/to/transcriptome
create-bam,true

[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,
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.

Copy
[gene-expression]
reference,/path/to/transcriptome
create-bam,true

[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,
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,

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