Trimmomatic for RNA-seq or Whole genome seuencing or for both?

Question

[reza]

hi

i want to use trimmomatic for trimming whole genome sequencing reads (illumina platform), But I've seen that trimmomatic mostly used in RNA-seq projects.

my question: can i use trimmomatic in my whole genome sequencing project?

[Matteo Schiavinato]

For future times, when you edit the original question don't delete the previous one, add an "EDIT" chapter at the end and start adding sentences. Otherwise future readers will not get the connection between my answer and your question, since mine was based on your previous statements.

Answer 1

[Matteo Schiavinato]

I think everything you need is here: http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf

A quick google + look at the manuals can save you a lot of time!

For what concerns suggestions to "improve reads", first I would say improve trimming, because the reads cannot be improved (they are what they are). To improve the trimming it always takes a couple of tryouts, depending on what are your reads, the chemistry of sequencing, the length, the average quality. Perhaps run fastqc on the reads, see what kind of problems they have, and adjust the strategy!

FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Answer 2

[harold.smith.tarheel]

Yes, you can use Trimmomatic for whole-genome sequencing (as well as RNA-Seq).