I need help to write a
for loop to run Trimmomatic tool for quality trimming of paired end fastq files.
Input: file01_R1.fastq, file01_R2.fastq.
The first file contains first read of paired end reads and the second file contains second reads. I have 100 input files in the same directory (50 files contain *e.R1g.fastq and another 50 files, file02_R1.R2fastq, file02_R2.fastq suffixes) and so on.
Output: file01_R1_PE.fastq, file01_R1_SE.fastq, file01_R2_PE.fastq, file01_R2_SE.fastq
PE = paired end
SE = single end
I need to write a for loop so that I can run an executable for all 100 files. Any help please! Thanks!