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Example Config CSVs for TRG/D Enriched Libraries

Example Config CSVs for TRG/D Enriched Libraries

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 customize text 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 create-bam,true [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 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,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 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,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,

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