contamination with barcodes in 3' prime end (R2)- 10x libraries

Question

[diglet27]

Hi there! After doing fastqc on my data (10x) I detected some Illumina adapters in R2. I was wondering if that probably means that I have also barcode contamination on the 3 'end of R2?

Thanks

[GenoMax]

Probably no need to do QC with FastQC on 10x data. You should proceed with cellranger (or other) analysis.

[swbarnes2]

Cellranger uses STAR, which in my experience is robust to that kind of problem. It will soft clip that sequence at the end, no problem.