Appropriate Trimming Parameter

Question

[Bio_Crap]

Hi, I just received the raw sequence data from shotgun metagenomic sequencing. Most of them are collected from cattle feces. And I want to study antimicrobial resistance profiles. However, I am not sure which trimming parameter I should use. I use trimmomatic, and my current setting is ''SLIDINGWINDOW：4：20 MINLEN 50" I look forward to your advice.

[rpolicastro]

Try not to delete posts if someone has answered.

Answer 1

[GenoMax]

As long as you manage to get rid of any adapter sequence present you don't need to use any additional parameters.

I will recommend that you try bbduk.sh fro BBMap suite. Parameters are easy to understand and a guide is available to help.