Question: The Illumina Experiment Manager (IEM) sample sheet asks for adapter sequences. What sequences do I use for adapter trimming?
Answer: Leave the line blank. We generally do not recommend any adapter trimming or preprocessing FASTQ reads before input to our 10x Genomics software pipelines. Trimming adapters from reads increases risk of cutting into the 10x barcodes and the UMIs and losing data.
If you are using an Illumina sample sheet for demultiplexing with bcl2fastq, BCL Convert or our mkfastq pipeline, please remove these lines:
Adapter or AdapterRead1 or AdapterRead2 under the
[Settings] section.