This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Appropriate Trimming Parameter

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.

genome next-gen gene sequence sequencing
• 1,378 views • link
updated by rpolicastro rpolicastro • written by Bio_Crap • Bio_Crap

Try not to delete posts if someone has answered.

• 0 views • link
written by rpolicastro rpolicastro

1 answer

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.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this