Fastqc of the fastq file
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
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Please use How to add images to a Biostars post to add images. You can't attach files to biostars posts.
thanks for your suggestion. Here is the link for png file. https://i.ibb.co/4tP3v7X/per-base-quality.png
Please read the post that genomax linked to and upload your image properly.
Hello RamRS, I have edited my post. I am sorry this is my first post and first analysis.
What type of data is this?
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.
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?
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.