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Cell Ranger


Loupe

10x Genomics
Chromium Single Cell Immune Profiling

Example Config CSVs for TRG/D Enriched Libraries

The multi pipeline

The cellranger multi pipeline analyzes multiple library types together, enabling more consistent cell calling between the V(D)J and gene expression data.

Visit the multi pipeline page to learn more about the arguments required to run cellranger multi.

T cell gamma-delta (TRG/D) multi config CSV examples

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.

LibrariesMulti config CSV


[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,

Back to the cellranger multi pipeline page