Hi, I have some RNA-seq datasets and I wanted to remove adapters and low quality bases before proceeding with my analysis. The final goal of my analysis is to perform differential gene expression between my control and experimental conditions. I used fastqc to check the quality of my sequences and it looks good. The links to the fastqc results for one of my samples is here:
I next removed adapters and low quality bases using a sliding window of 4:30 using trimmomatic, but after trimming I only have 87% of my reads remaining. Could someone please explain why trimmomatic is removing over 10% of my reads even though the quality of my raw sequences is pretty good?
This is the command for trimmomatic:
java -jar trimmomatic-0.39.jar PE -threads 32 -trimlog SF1-1-C-gill_trimlog.log -summary SF1-1-C-gill_summary.txt SF1-1-C-gill_R1.fastq.gz SF1-1-C-gill_R2.fastq.gz SF1-1-C-gill_r1paired.fastq.gz SF1-1-C-gill_r1unpaired.fastq.gz SF1-1-C-gill_r2paired.fastq.gz SF1-1-C-gill_r2unpaired.fastq.gz ILLUMINACLIP:20:30:15:8:true SLIDINGWINDOW:4:30
I am using trimmomatic version 0.39