Cellranger: BCR analysis

Question

[bsmith030465]

Hi,

Sorry for the newbie question. I am just getting started with scRNA analysis.

I have fastq data for one sample (in folders Cobin_72_GEX, Cobin_72_BCR and Cobin_72_FB). I would like to get the count matrices. My questions:

1. Is BCR to be processed the same way as gene expression (GEX)?
2. My files are library and feature files are:

BCR_libraries.csv:

fastqs,sample,library_type
Cobin_72_BCR,Cobin_72_BCR,Gene Expression
Cobin_72_FB,Cobin_72_FB,Antibody Capture

FB_features.csv

id,name,read,pattern,sequence,feature_type
FB1,H1_tet,R2,5PNNNNNNNNNN(BC),GTCCGACTAATAGCT,Antibody Capture
FB2,NP_tet,R2,5PNNNNNNNNNN(BC),AACCTTTGCCACTGC,Antibody Capture
FB3,H3_tet,R2,5PNNNNNNNNNN(BC),CAGGTTGTTGTCATT,Antibody Capture

Does this command look ok to process BCR?

cellranger count --id=Cobin_72_BCR_out \
    --transcriptome=/home/data/references/refdata-gex-GRCh38-2020-A \
    --libraries=BCR_libraries.csv \
    --feature-ref=FB_features.csv

thanks!

[GenoMax]

Check this link, for VD(J) analysis. For Feature Barcoding this page.

Answer 1

[swbarnes2]

cellranger count is what you want for the gene expression libraries, but there is a cellranger vdj, which is probably what you want for the BCR sample. I don't know about the antibody capture. What I suggest you do is find out the name of the kits used for each sample, and ask 10XGenomics what to do.

Answer 2

[tiago211287]

You can use cite-seq-Count to quantify the antibody tags and generate an 10x-like output that can be easily imported to R using the Seurat package.

Software: https://github.com/Hoohm/CITE-seq-Count

Tutorial: https://hoohm.github.io/CITE-seq-Count/Running-the-script/

[xuyingzheng4321]

Hi there, I am trying to understand the input of CITE-seq-Count and find it quite confusing. I have GEX, ADT and HTO fastq files(I1, R1, R2) from a partner lab. Could you provide any insights on what should be inputed to CITE-seq-Count as arguments?