{"folder":{"article_order":1,"category_id":14000075212,"created_at":"2021-06-25T00:38:01-04:00","description":null,"id":14000127537,"is_default":false,"name":"Celllranger Single Cell RNA-Seq FAQ","position":5,"updated_at":"2021-06-25T00:38:01-04:00","visibility":1,"published_articles":[{"art_type":1,"created_at":"2021-06-25T00:42:07-04:00","current_child_thumbs_down":0,"current_child_thumbs_up":0,"desc_un_html":" 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 ","description":"

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


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