Per base sequence quality - fastqc

Question

[bioinfo223]

Hi everyone, I am new to bioinformatics, I am asking a very basic question here, I have paired-end fastq data, I did fastqc, and in this per base sequence quality, few reads are in the red region, and there is no adapter and overrepresented sequence. should I do the trimming of my read? if I should then what parameter I should give in trimmomatic?

[GenoMax]

Several blog posts from authors of FastQC that you will find of interest here: https://sequencing.qcfail.com/software/fastqc/

Answer 1

[Buffo]

I would suggest you read the manual, it is very well explained and easy to use. Your reads look very good to me, the boxplot shows that most of your reads have a quality equal to or greater than 28, some "outliers" don't, but I would not consider trimming or filtering is needed.

Answer 2

[kenneditodd]

Always trim!!! Even if you already have good quality. I use BBDuk to trim. They should have a recommended pair end sequencing command to run in the docs.