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Trim the reads in loop using Trimmomatic !

  • Public
By Neel 1190 days ago
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