I have also tried to use the command line without including a path to my original read files, seen below: java -jar $trimmomatic PE -phred33 240_CTTGTA_L004_R1_ C240_CTTGTA_L004_R2_ C240_CTTGTA_L004_R1. C240_CTTGTA_L004_R1. C240_CTTGTA_L004_R2. C240_CTTGTA_L004_R2. ILLUMINACLIP:TruSeq-PE.fa:2:30:10 I am using Trimmomatic-0.36 and also undertaking this command on a remote server, rather than my local drive. I am very new to Bioinformatics and especially new to programming, so I would appreciate if you can try to defer from using any jargon so I can understand your points easier. I am a university student currently trying to use Trimmomatic for the first time and have attempted to use a command line I have formed from using the official Trimmomatic manual and some other online resources.
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