Question: contamination with barcodes in 3' prime end (R2)- 10x libraries
gravatar for diglet27
6 weeks ago by
diglet270 wrote:

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?


sequencing • 129 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by diglet270

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by genomax89k

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.

ADD REPLYlink written 6 weeks ago by swbarnes28.6k
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