This will involve getting bcl-convert to produce fastqs for the index read. however, I could only get bcl2fastq to do it, not bcl-convert, so we might want to change to bcl2fastq, the older software.
We can then use fastqc or fastp on the index reads.
This will involve getting bcl-convert to produce fastqs for the index read. however, I could only get bcl2fastq to do it, not bcl-convert, so we might want to change to bcl2fastq, the older software.
We can then use fastqc or fastp on the index reads.