Oh I see. But how do I then provide the output such that I get a new file for every file that is being trimmed?
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Trimmomatic can't seem to find my adapter files, and I've tried a lot of different pathways but nothing works. Any help is appreciated, thanks.
Here's my code:
for file in ../../fqgz_trim_single/*R1_001.fastq.gz
do
trimmomatic SE -threads 1 -phred33 -trimlog $file ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:100 CROP:100
done
The adapters are located in the same folder as the raw reads. If I change the pathway to ../../TruSeq3-SE.fa:2:30:10 that doesn't work neither.
Thanks
The syntax is
java -jar trimmomatic-0.35.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Here, trimmomatic SE -threads 1 -phred33 -trimlog $file ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEA... you don't provide any output file.
Oh I see. But how do I then provide the output such that I get a new file for every file that is being trimmed?
Use a loop to loop through your files. See: How to loop to use trimmomatic for multiple fastq files?
Thank you!
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