Illumina does not equal reads PF with real number of reads

Question

[Paul]

Dear users,

In Illumina BaseSpace indexing ID is total number of passing reads (reads PF). When I take all my fastq files and sum all the reads, this numbers suppose to be equal? Is that true? I am just asking because I have totally different numbers. Thank you for discussion or advices.

[Devon Ryan]

I've never used base space, but make sure you're not double counting paired-end reads, since the pass filter metric is at the cluster level (I think).

[Paul]

Hi Devon, you are right, it is just one read and also in the sum is Undetermined fastq files. Thank you for reply.