I have ran this script.
java -jar trimmomatic-0.35.jar PE -phred33 -trimlog /home/richardsonlab/AMMA_transcripts/trimmo30trimlog.txt /home/richardsonlab/AMMA_transcripts/R1V22_B9F8St_ACTTGA_L002_R1_001.fastq /home/richardsonlab/AMMA_transcripts/R1V22_B9F8St_ACTTGA_L002_R2_001.fastq pairedoutput1 unpairedoutput1 pairedoutput2 unpairedoutput2 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:45
I can view the trim log Trimmomatic spit out, however, where can I find my newly trimmed reads? I would like to run them through QC in galaxy. Also, can anyone explain to me what I am looking at in the trim log?
Thanks for your help, Nikelle