Question: Trimming didnt work
0
gravatar for Kiki_01
3 days ago by
Kiki_010
Kiki_010 wrote:

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 :)

rna-seq • 70 views
ADD COMMENTlink modified 3 days ago by genomax78k • written 3 days ago by Kiki_010
1
gravatar for genomax
3 days ago by
genomax78k
United States
genomax78k wrote:

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.

ADD COMMENTlink written 3 days ago by genomax78k

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?

ADD REPLYlink written 3 days ago by Kiki_010

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

ADD REPLYlink modified 3 days ago • written 3 days ago by genomax78k

Obraz1 obraz3

ADD REPLYlink modified 3 days ago by genomax78k • written 3 days ago by Kiki_010

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

ADD REPLYlink modified 3 days ago • written 3 days ago by genomax78k

Thank you for your help!

ADD REPLYlink written 3 days ago by Kiki_010
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