Meta-analysis using 16S rRNA NGS data

Question

[bala]

Hi everyone

I am running a meta-analysis using 16S rRNA NGS data, most of the file have not primer information in their corresponding papers.

Kindly suggest me is their any tool that automatically detect and remove 16S primer from the sequence.

By the way i am using DADA2 for downstream process, (filterandtrim can be used to remove primer by trim =c(19,17 )) But, I want to remove primer before DADA2.

I have tried with rbind option with known V4 primers, but it's not working.

Thank you for your time and suggestion

Answer 1

[Antonio R. Franco]

Use a regular filter such as Cutadapt, Trimmomatic, Trim-Galore or the like to this end