Low percentage of 'Fraction Antibody Reads Usable' in Feature Barcode Cell Ranger output

Question

[rocio.castellanos]

Hi, I have a question regarding the Cell Ranger output of scRNAseq with Feature Barcode. I've performed the standard Cell Ranger count using cellranger-6.0.0 and the following arguments:

--id=A_GEX
--libraries=library_A.csv
--transcriptome=/....../refdata-gex-GRCh38-2020-A
--feature-ref=/...../10x_feature_ref.csv

When looking at the output QC I've noticed that the antibody sequencing parameters show good sequencing quality. However, the "Fraction Antibody Reads Usable" is very low.

When looking at the count matrix every feature barcode is counted, so the barcodes in the 10x_feature_ref.csv seem to be correct.

Is there any reason why this is happening? or is there any way to solve it?

Thank you in advance

[sejjgva]

Did you manage to find out why this is happening? I have something similar going on and can't quite figure out the issue.