Question: I am getting the following error running cellranger-arc
count. The ATAC sequencing parameters were done correctly: 50x8x24x49
[error] Error processing ATAC FASTQ files with specified parameters on machine xxx:
FASTQ file = /path/to/outs/fastq_path/ATACdata_S1_L002_R2_001.fastq.gz
I2 read length = 15
The I2 read must be at least 16 bases long. This could be caused by ATAC and Gene Expression flow cells having been swapped.
Answer: Looking at the sample sheet CSV used for demultiplexing, some customers choose to use the IEM (Illumina Experiment Manager) format. The Illumina IEM format sometimes has a setting to trim adapters from read 1 and read 2:
The output from this sample sheet is not compatible with the Cell Ranger ATAC or Cell Ranger ARC pipelines. We do not recommend using the Adapter trim setting. The reason for this error is that the 10x barcode is located in the R2 read. If these reads are trimmed, looking at the fastqc profile, there will be a range of lengths rather than a single read length. This is not compatible with the Cell Ranger ARC or Cell Ranger ATAC pipelines, which expects there to be reads all with the length 16 bp.