How to Choose Trimmomatic Min Length Parameter

Question

[Eliveri]

I have paired sequences with 150 bp in length. The adapter is the Universal Illumina adapter (~35 bp).

My final goal is to filter out reads after mapping to a reference genome. I am using Trimmomatic to first trim the adapters. What is a good MINLEN to define for Trimmomatic? The Minimum length I currently defined is 100.

Or is it not necessary to define a minimum length as the next step is mapping? Will keeping too many short reads slow down mapping? Thank you.

Answer 1

[shelkmike]

I recommend not to set MINLEN at all. All read aligners that I'm aware of have some inner thresholds for the minimimum read length. Hence, very short reads won't be aligned anyway.