are forward and reverse read counted as a single read?

[Rob_DNA]

Hello,

when inspecting the denoising stats from dada2, I am wondering if the forward and reverse read are counted as a single read. Below I've added an image of a part of the stats output. Let's take a look at sample PD1_A1. The total number of reads of this sample is 211092 (I assume half of it are forward reads and the other half are reverse reads). After filtering and denoising, 162356 reads are left. Then merging is performed and this results in a total of 113814 reads after merging.

However, if the 162356 reads before merging consist of approximately half forward and half reverse reads, wouldn't you at least expect for the number of reads to be halved after merging? So in that case you would have a maximum of 81178 (=162356/2), because 2 reads (fw and rev) are merged to a single read.

Am I interpreting the stats output incorrectly?

Thank you!

Kind regards,
Rob

[timanix (Timur Yergaliyev)]

Hi!
The terminology is a little bit confusing here. Hope that I will be able to clarify it.

@Rob_DNA

The total number of reads of this sample is 211092

I think you should interpret it as number of read pairs, not as a summary of forward and reverse reads separately.

@Rob_DNA

After filtering and denoising, 162356 reads are left.

Read pair will be discarded if any (forward or reverse) read from the pair is dropped.

@Rob_DNA

Then merging is performed and this results in a total of 113814 reads after merging.

Here it is a count of pairs that were successfully merged to one longer sequence.

[Rob_DNA]

Thank you for the clarification timanix!