16 EMP - Adaptor timming

[fconstancias]

Dear EMP protocol users,

We are using the EMP protocol (515F - 806R, forward-barcoded) to generate 16S libraries.

I am not sure which sequence/tool should I use for adaptor trimming when using the protocol. Do you have any recommendation?

Thanks

[justinshaffer]

Hello, We recommend using QIIME 2's demux plugin's emp-paired or emp-single method, depending on whether your sequence data are paired or not. https://docs.qiime2.org/2022.11/plugins/available/demux/ This approach will demultiplex your reads and trim primers and adapter sequences, but only works for data generated using the EMP protocol as you are. If other library construction methods are used we recommend using QIIME 2's cutadapt plugin for removing adapter and primer sequences. Best wishes, Justin

…

On Wed, Jan 18, 2023 at 12:48 AM Florentin Constancias < ***@***.***> wrote: Dear EMP protocol users, We are using the EMP protocol (515F - 806R, forward-barcoded) to generate 16S libraries. I am not sure which sequence/tool should I use for adaptor trimming when using the protocol. Do you have any recommendation? Thanks — Reply to this email directly, view it on GitHub <#130>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADSDCGED6QOXLAGSRG5P4OLWS6U6DANCNFSM6AAAAAAT6ZVGIE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Justin Shaffer, PhD Postdoctoral Researcher Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com