Trimmomatic and bwa-mem

I uploaded my ngs data files in Galaxy and then ran fastqc to check the quality of both files. According to fastqc report, fasq files contain adapter sequences that I need to removed so I used Trimmomatic. But Trimmomatic produced 4 files:R1 paired , R2 paired , R1 unpaired and R2 unpaired. Which of these 2 files I can use in bwa mem for alignment?

Hi @Anas_Jamshed
use paired files. Unpaired file contain singleton reads that lost paired read during the trimming.
Kind regards,

Thanks. My 2 fastq trimmed files(R1 paired, R2 paired) have almost 15 GB in size so when I am aligning them with reference Genome, it is taking too much time. How much time normally it takes for alignment? 12 hours or one day?

How long a job queues, then how long it executes, can vary. Please try searching this forum with the tag I added to your other post Alignment time in galaxy