Fastqc of the fastq file

Question

[sgadila]

Hello,

I was wondering if I need to trim low quality bases from my fastq file that has an average quality of 30. However, the bases after position 62 has a quality of 20 and below. After trimming, I am loosing almost 20% of the total reads. I have attached the Fastqc result of my Fastq file below. Thanks for your help.

Thanks, Shiva

[GenoMax]

Please use How to add images to a Biostars post to add images. You can't attach files to biostars posts.

[sgadila]

thanks for your suggestion. Here is the link for png file. https://i.ibb.co/4tP3v7X/per-base-quality.png

[Ram]

Please read the post that genomax linked to and upload your image properly.

[sgadila]

Hello RamRS, I have edited my post. I am sorry this is my first post and first analysis.

[rpolicastro]

What type of data is this?

[sgadila]

I ran Fastqc on the reads from the sequencer before trimming low quality bases. Total RNA-seq library prepared from gram-negative bacteria and single end 75bp reads were generated using Illumina nextseq.

[GenoMax]

It is normal to see whiskers on the Q-score box plot like that. Are you aligning to a reference, if so the aligner should be able to soft-clip those bases, if they are not matching the reference.

To reconcile 20% data loss you mention, are you removing entire reads that have low scores on the ends?

[sgadila]

Yes I will be aligning this data to the reference genome. I trimmed the low quality bases using trimmomatic and Illuminaclip to remove adapter sequences. For trimmomatic, I used SLIDINGWINDOW:4:30.