Trimming didnt work

Question

[Kiki_01]

Hi! Im new here. I started doing the RNA-Seq analysis. I have data from Illumina. I did the quality control with fastqc and tried to trim it using trimmomatic program and my data didnt change at all. I take under consideration that maybe i should change the values i used. Heres the command i used. I would appreciate every help.

java -jar /path../Trimmomatic-0.39/trimmomatic-0.39.jar PE UP1_1.fastq UP1_2.fastq UP1_trimmed_1.fq UP1_unpaired_1.fq UP1_trimmed_1.fq UP1_unpaired_2.fq ILLUMINACLIP:adapter.fa:2:30:5

Is it possible that i dont need to trim my data? Thanks for every respond :)

Answer 1

[GenoMax]

I did the quality control with fastqc and tried to trim it using trimmomatic program and my data didnt change at all

Your data does not necessarily need to have contamination/extraneous sequences. It may be clean and can be used for further analysis.

[Kiki_01]

By the report I got I think it looks nice, but I thought anything it would change. Report is the same as before the trimming one. Maybe the values I used were not strick enough for my data?

[GenoMax]

If you show us the before report from FastQC, it would be useful. Add images for per base sequence quality, per base sequence content using these directions: How to add images to a Biostars post

[Kiki_01]

[GenoMax]

Your data looks clean. You can move on to next step of alignment.

[Kiki_01]

Thank you for your help!