BOL: Trim the reads in loop using Trimmomatic !

BioScripts
Neelam Jha
Trim the reads in loop using Trimmomatic !

Trim the reads in loop using Trimmomatic !

By Neelam Jha 965 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