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:
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