I get almost the same fastqc report for a fastq file before and after using TrimGalore

Question

[mohamedrefaat.1.1992]

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

[lakhujanivijay]

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.

[Joe]

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)

[WouterDeCoster]

How to add images to a Biostars post

[dschika]

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.