Feature Reference CSV is passed to cellranger count with the --feature-ref flag and declares the set of Feature Barcode reagents in use in the experiment.
For each unique Feature Barcode used, this file declares a feature name and identifier, the unique Feature Barcode sequence associated with this reagent, and a pattern indicating how to extract the Feature Barcode sequence from the read sequence.
Required Columns for Feature Reference CSV File
Column Name | Description |
id | Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome. |
name | Human-readable name for this feature. Must not contain whitespace. This name will be displayed in Loupe Browser. |
read | Specifies which RNA sequencing read contains the Feature Barcode sequence. Must be R1 or R2. Note: in most cases R2 is the correct read. |
pattern | Specifies how to extract the Feature Barcode sequence from the read. See the Barcode Extraction Pattern section below for details. |
sequence | Nucleotide barcode sequence associated with this feature. E.g., antibody barcode or sgRNA protospacer sequence. |
For Example: A valid Feature Reference CSV File for Antibody Capture barcode will be as shown in the table below
id | name | read | pattern | sequence | feature_type |
CD3 | CD3_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | AACAAGACCCTTGAG | Antibody Capture |
CD4 | CD4_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | TACCCGTAATAGCGT | Antibody Capture |
CD8a | CD8a_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | ATTGGCACTCAGATG | Antibody Capture |
CD14 | CD14_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | GAAAGTCAAAGCACT | Antibody Capture |
CD15 | CD15_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | ACGAATCAATCTGTG | Antibody Capture |
CD16 | CD16_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | GTCTTTGTCAGTGCA | Antibody Capture |
CD56 | CD56_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | GTTGTCCGACAATAC | Antibody Capture |
CD19 | CD19_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | TCAACGCTTGGCTAG | Antibody Capture |
CD25 | CD25_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | GTGCATTCAACAGTA | Antibody Capture |
CD45RA | CD45RA_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | GATGAGAACAGGTTT | Antibody Capture |
CD45RO | CD45RO_TotalSeqB | R2 | 5PNNNNNNNNNN(BC)NNNNNNNNN | TGCATGTCATCGGTG | Antibody Capture |
For more information on creating Feature Reference CSV File, follow the below link
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref