Can anyone recommend a guide for choosing values for parameters when using Trimmomatic? I ran fastqc on the sequences after converting them to fastq format, and the results seemed to indicate the presence of adapter sequences. I am processing single-end reads (from a tomato seedling RNA-seq experiment, http://www.ncbi.nlm.nih.gov/sra/?term=SRR948460). I could not find a guide explaining in-depth what each parameter means, and I'm not sure how to decide besides trial and error (except I know to specify SE and -phred 33). Thank you!