Hello, My Illumina paired-end reads (version 1.9) length various between 35-151. I noticed that the forward and reverse reads do not have the same length. Here are the Fastqc quality plots for R1 and R2.
Is the following Trimmomatic command optimal set to run for the above QC plots and used the trimmed reads for assembly?
java -jar /programs/trimmomatic/trimmomatic-0.32.jar PE -phred33 paired_end_reads_1.fastq paired_end_reads_2.fastq kept_paired_end_reads_1.fastq kept_paired_end_reads_2.fastq unpaired_1.fastq unpaired_2.fastq SLIDINGWINDOW:4:15 MINLEN:65
Thank you in advance.