How to Choose Trimmomatic Min Length Parameter
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.
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