How to run Trimmomatic with multiple files in a loop

Question

[Kumar]

Hi, I am trying to run the Trimmomatic for multiple fastq.gz files. So, I am trying to run it in a loop at bash script. Please suggest ways to improve the code that I am using below. Please note that I have basic skills in bash script so the code has silly mistakes.

for i in *_R1.fastq
do

java -jar /media/Data/apps/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 ${i}.1.fastq.gz ${i}.2.fastq.gz ${i}.trimmed_R1.fastq.gz 
${i}.untrimmed_R1.fastq.gz ${i}.trimmed_R2.fastq.gz ${i}.unpaired_R2.fastq.gz SLIDINGWINDOW:4:20 MINLEN:150 
ILLUMINACLIP:/media/Data/apps/Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:40:15

done

[Mensur Dlakic]

You keep asking variations of the same question. By now you should be able to troubleshoot these on your own. As I advised before, and cpad0112 reminded you, try these commands inside echo. You should be able to see instantly if the output is as intended.

[cpad0112]

do an echo. Use threads and specify the RAM for Trimmomatic

[Pierre Lindenbaum]

how is your problem different from your previous question ? How to run Unicycler for hybrid assembly with multiple samples