Illumina does not equal reads PF with real number of reads
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.
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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).
Hi Devon, you are right, it is just one read and also in the sum is Undetermined fastq files. Thank you for reply.