No change in quality score graph even after adapter removal

Question

[Sreedevi]

First I performed fastqc for my fastq file Then I found that there is adapter content from the fastqc report. I removed the adapter content using trimmomatic and performed fastqc on the output file Here the output file showed that the earlier adapter content is removed but there is no change in quality score graph between the two.Does this mean that adapter removalt was not successful?

Answer 1

[dsull]

Adapters have nothing to do with quality scores. Your adapter removal was successful.

Quality scores means how confident we are that an A in our FASTQ file is actually an A, a T is actually T, a C is actually a C, and a G is actually G.

This is a process called "base calling". A sequencing machine is kind of like a camera taking photos of nucleotides. If the photo is blurry, it's impossible to determine whether something is an A or a G. That's what poor quality means. The "score" itself reflects the probability that we got the nucleotide wrong.

In your FASTQ file, you might see a sequence like NATCGTAGCGNNNCATN. Those N's are "poor quality" so we can't actually tell what base they are (is it an A, T, C, or G?).