Question: contamination with barcodes in 3' prime end (R2)- 10x libraries
0
gravatar for diglet27
6 weeks ago by
diglet270
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?

Thanks

sequencing • 129 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by diglet270
2

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
1

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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