Question: Fastqc of the fastq file
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gravatar for sgadila
25 days ago by
sgadila0
sgadila0 wrote:

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

Fastqc per base quality

rna-seq • 125 views
ADD COMMENTlink modified 25 days ago • written 25 days ago by sgadila0

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

ADD REPLYlink written 25 days ago by genomax92k

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

ADD REPLYlink written 25 days ago by sgadila0

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

ADD REPLYlink written 25 days ago by RamRS30k

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

ADD REPLYlink written 25 days ago by sgadila0

What type of data is this?

ADD REPLYlink written 25 days ago by rpolicastro2.3k

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.

ADD REPLYlink modified 25 days ago • written 25 days ago by sgadila0

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?

ADD REPLYlink written 25 days ago by genomax92k

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.

ADD REPLYlink written 25 days ago by sgadila0
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