How to run Trimmomatic with multiple files in a loop
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
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do an echo. Use threads and specify the RAM for Trimmomatic
how is your problem different from your previous question ? How to run Unicycler for hybrid assembly with multiple samples
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.