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

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2.5 years ago

rocio.castellanos • 0

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.

enter image description here

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

scCITE-seq feature-barcode 10x scRNA-seq • 1.5k views

ADD COMMENT • link updated 5 weeks ago by octopuslegs11 ▴ 10 • written 2.5 years ago by rocio.castellanos • 0

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

ADD REPLY • link 2.0 years ago by sejjgva • 0

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I don't want to piggyback on this but did you figure out what the issue was? I'm also experiencing this issue!

ADD REPLY • link 5 weeks ago by octopuslegs11 ▴ 10

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