Difference in quality between forward and reverse pairs

[benine]

I've noticed when trimming Illumina reads with Trimmomatic, there are almost always more Forward-Only surviving reads than Reverse-Only surviving reads. I was just wondering what the reason for this was.
I'm a computer tech so maybe I'm missing something on the Illumina side or maybe it's in Trimmomatic. Either way I'm curious.

[dpryan]

That's completely normal. There's an extra step involved to reverse complement the fragments so you can sequence read #2 and this decreases the quality.

[Brian Bushnell]

If you are talking about quality trimming, Read 2 typically has lower quality and thus is more likely to be trimmed shorter.

[benine]

Ya I figured it was just something involved in the sequencing but I just wanted to clarify. Thanks guys.