Question: I get almost the same fastqc report for a fastq file before and after using TrimGalore
0
gravatar for mohamedrefaat.1.1992
4 weeks ago by
mohamedrefaat.1.19920 wrote:

Hi everyone, I'm using trimGalore to remove adaptors and trim low quality reads.

The problem is that I get almost the same output after quality control as before it.

Can anyone tell what's the problem ?

This the command I used

$ trim_galore --fastqc --illumina 23_S19_L001_R2_001.fastq.gz -q

before quality control :https://s9.postimg.cc/7aku795yn/before.png

after quality control :https://s9.postimg.cc/93nqvaohr/after.png

fastqc trimgalore • 145 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by mohamedrefaat.1.19920
1

Strange that it worked for you without specifying quality INT in -q option. It failed in my case

$ TrimGalore-0.4.5/trim_galore --fastqc --illumina ../test.fq -q
Option q requires an argument
Please respecify command line options

I checked the help

$ TrimGalore-0.4.5/trim_galore -h

 USAGE:

trim_galore [options] <filename(s)>  

-q/--quality <INT>      Trim low-quality ends from reads in addition to adapter removal.

Can you check once again?

UPDATE

Specifying -q works and only towards end of the reads. But I need to confirm.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Vijay Lakhujani2.5k
1

Are you sure you need to remove adapters? That may already have been done by the sequencing machine (in which case you probably won't see much difference in QC)

ADD REPLYlink written 4 weeks ago by jrj.healey4.6k

How to add images to a Biostars post

ADD REPLYlink written 4 weeks ago by WouterDeCoster29k

The result of the trimming looks ok for me.

The quality of your data set is not the best. Removing adaptors and trimming low quality ends from reads (-q) leads to an increase in the overall mean quality values towards the end, which is visible in after.png. Given the before.png result, I would not expect too much.

ADD REPLYlink written 4 weeks ago by dschika290
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