the v_gene is None in all of samples with the command of cellranger vdj

[WellJoea]

IN=PATH/RawData ID=$1 VDJ38=PATH/refdata-cellranger-vdj-GRCh38-alts-ensembl-3.1.0 CR=PATH/cellranger-3.1.0/cellranger $CR vdj --id=${ID}_vdj \ --fastqs=$IN/${ID}-1,$IN/${ID}-2,$IN/${ID}-3,$IN/${ID}-4 \ --sample=${ID}-1,${ID}-2,${ID}-3,${ID}-4 \ --reference=$VDJ38

I use the command to annotate the vdj fastq, but all of the samples is None in v_gene column

[WellJoea]

The v gene is none because the illumina PE seq cannot read though all of the cdr3 region?

[wyattmcdonnell]

Hi @WellJoea what kind of cells are you working with?