Filtered and denoised reads

[Yogesh_Gupta (Yogesh)]

From dada2 result table, it looks like filtered and denoised read is the

same.

Please correct me if I am wrong?

[thermokarst]

@Yogesh_Gupta

it looks like filtered and denoised read is the same.

Yep! That means that all of the reads that passed the filtering step also passed the denoising step. You lost 0% of your reads on denoising.

[Yogesh_Gupta (Yogesh)]

Hi @thermokarst,

Thanks, I am actually not able able to understand what exactly it does at the filtering step and then at denoising step?

How the filtering is separated from denoising?

Regards
Yogesh

[yakshi.ortiz]

Hi Yogesh,

If I understand right, what the denoising step does is to correct sequencing errors at nucleotide level. This is why you will see very low to no loss at this step. The filtering step removes sequences based on the selected max-ee value. The max-ee is the sum of probabilities that each of your nucleotides were called incorrectly (this is based on the phred score of each of your nucleotides in a given sequences). If that sum is more than the selected max-ee, then your sequence is discarded. You can read more at this link.

I hope that helps you a bit!
Yakshi