NextSeq reads count

[PJohn]

Hi all,

I counted the number of reads in the same sample in 2 different ways:

a) On the sequencer (NextSeq), by counting the number of reads identified that passed filter
b) On the server, in the fastq files using the command wc –l (total lines) and then dividing the result by 4

The problem is that those two numbers do not match. Shall they match or not? What is the difference? My objective is to get around 50 million reads per sample and I am figuring out which counting option use. Thanks!

PJ

[GenoMax]

Are you doing adapter trimming on the sequencer? I assume the difference may be explained by reads that passed filter but were trimmed due to presence of adapter/dimers.