trimmomatic offering different results on galaxy vs actual


When I attempt to trim reads via galaxy vs. command line, I get different results with a near 2000 BP difference.

These are the commands I used:

command line:

java -jar /software/trimmomatic/0.39/trimmomatic-0.39.jar PE ERR048396_1.fastq ERR048396_2.fastq trial2.trimmed.paired.R1.fastq trial2.trimmed.unpaired.R1.fastq trial2.trimmed.paired.R2.fastq trial2.trimmed.unpaired.R2.fastq ILLUMINACLIP:TruSeq3-PE-2.fa:2:40:15:8:True LEADING:15 TRAILING:15 SLIDINGWINDOW:4:20 MINLEN:35

This is what I set my galaxy options to, which should be the same as what I have set my command line to do.

I did download these sequences from galaxy and moved them to a remote server, prior to doing that, however, I made sure to fastqc both sets of data to ensure I have the same data in each.

Any idea where/if I’ve done something wrong? Any help would be greatly appreciated

Hi @drip2hardpanu
do you use the same version of Trimmomatic?
I believe, Trimmomatic applies rules in the specified order, at least in Galaxy. It might be the case on command line, but I have not tested it. You have different order of trimming rules on command line and Galaxy. Maybe swap ‘rules’ on command line and check if you get different output.
Hope that helps.
Kind regards,


you were indeed, very correct

Thank you!!