How do I check the quality of merged fastq sequence?

Hi, I am Yunju.

My data is paired-end data which was generated from Illumina miseq.

During the DADA2 step, I can do filter, remove chimera, and also merge two forward and reverse fastq files to 1 merged fastq.

But how do I check the quality of merged fastq and see the quality in the

Thank you for reading this.
Best regards,

Hi @Yunju,

When the sequences become merged (after dada2’s denoising) they no longer have any quality information, so they become fasta files. Generally speaking any quality you see after merging is no longer going to be an instrument’s score but will become whatever the merging tool has provided for that base (assuming it provides one at all).

For dada2 specifically, it doesn’t really make sense to report quality scores after denoising because it does a lot of error correction on your reads which means the reads that it merges are not exactly the same as the sequenced reads. This means we’re now at least twice removed (after merging) from the sequencer’s quality scores and so these scores are no longer useful.

In short, there isn’t a way to view the merged quality because there really isn’t a useful definition of merged quality.


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