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:
- Is BCR to be processed the same way as gene expression (GEX)?
- My files are library and feature files are:
fastqs,sample,library_type Cobin_72_BCR,Cobin_72_BCR,Gene Expression Cobin_72_FB,Cobin_72_FB,Antibody Capture
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