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[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,
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[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,
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[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.
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|
[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,
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