Question on Trimmomatic Defaults?

Question

[nikelle.petrillo]

Hi everyone,

I am new to using trimmomatic, can anyone explain to me what the default settings are?

This is the command I used:

Trinity \
  --left R1V22_B9F8St_ACTTGA_L002_R1_001.fastq \
  --right R1V22_B9F8St_ACTTGA_L002_R2_001.fastq \
  --trimmomatic \
  --max_memory 10G \
  --CPU 16 \
  --seqType fq \
  --SS_lib_type RF \
  --output /home/richardsonlab/AMMA_transcripts/trinity_out_dir2 \
  --normalize_reads

I am just not entirely sure what running the --trimmomatic command actually did to my fastq files.

Thanks for your help!

Nikelle

[GenoMax]

If your data does not have have adapter contamination then it is not going to do anything to the data. That is normal behavior. Do you have a reason to suspect that there is something (e.g. adapters/low quality bases) in your data based on FASTQC report?

[nikelle.petrillo]

http://tinypic.com/r/21cti0/9

My FASTQC report looks like this on average for pretty much all of my raw files. Do you suggest not using any quality trimming/filtering?

Thanks for your help!
Nikelle

[GenoMax]

You should scan/trim (if needed) all data. Do it outside trinity if you want to see what happens.

Trimming would not occur if no adapter contamination is present. If you choose to trim based on Q-scores then use a low cut-off (e.g. Q-score 10 or less).