https://bioinformaticsonline.com/snippets/view/43397/trim-the-reads-in-loop-using-trimmomatic? https://bioinformaticsonline.com/snippets/view/43397/trim-the-reads-in-loop-using-trimmomatic Thu, 23 Sep 2021 13:13:38 -0500 https://bioinformaticsonline.com/snippets/view/43397/trim-the-reads-in-loop-using-trimmomatic for infile in *_1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq.gz \ ${base}_1.trim.fastq.gz ${base}_1un.trim.fastq.gz \ ${base}_2.trim.fastq.gz ${base}_2un.trim.fastq.gz \ SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15 done]]> Neel