Updating EMP500 methods to include 18S and ITS processing updates

[justinshaffer]

Hello @antgonza! Can you please review this and merge if acceptable? Thank you!

[justinshaffer]

Hi @cuttlefishh, @wasade, or @ElDeveloper - if possible please review and merge this update. It includes important changes for the 18S and ITS data processing for the EMP500. Thank you!

[justinshaffer]

Hi Daniel - thanks again for your comments on the updated methods for the EMP500. I've gone through and updated the pull request to include the changes you requested for the methods - is it OK to merge?

Thanks,

Justin

On Tue, Dec 6, 2022 at 8:21 AM Daniel McDonald @.***> wrote:

@.**** commented on this pull request.

In methods/methods_release2.md https://github.com/biocore/emp/pull/129#discussion_r1041184893:

-#### Taxonomic profiling - Process: Feature-classifier sklearn - Parameters: Using the UNITE 8 release as a reference +#### Denoising +`deblur workflow \

Qiita uses --min-reads 1 to avoid a study specific bias

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[wasade]

I'm not sure. The notebooks as is are not runnable as they depend on specific filepaths for a users account. However, if that is not a concern then yes?

[justinshaffer]

Thanks! Yes, I've noted the comments you made for the code that is already available merged to biocore, and have added making those changes to my list of action items for the next pull request. I think the main reason that code seems whacky in addition to the filepath issue you mentioend is that a lot of the Qiita functionality was not available when Luke was performing those analyses. Either way, I want to get the updated methods available on biocore sooner than later so will merge those changes as it seems we're on the same page.

Justin

On Tue, Dec 13, 2022 at 1:54 PM Daniel McDonald @.***> wrote:

I'm not sure. The notebooks as is are not runnable as they depend on specific filepaths for a users account. However, if that is not a concern then yes?

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[wasade]

Sounds good!

On Dec 13, 2022, at 1:58 PM, Justin Shaffer @.***> wrote:

Thanks! Yes, I've noted the comments you made for the code that is already available merged to biocore, and have added making those changes to my list of action items for the next pull request. I think the main reason that code seems whacky in addition to the filepath issue you mentioend is that a lot of the Qiita functionality was not available when Luke was performing those analyses. Either way, I want to get the updated methods available on biocore sooner than later so will merge those changes as it seems we're on the same page.

Justin

On Tue, Dec 13, 2022 at 1:54 PM Daniel McDonald @.***> wrote:

I'm not sure. The notebooks as is are not runnable as they depend on specific filepaths for a users account. However, if that is not a concern then yes?

— Reply to this email directly, view it on GitHub https://github.com/biocore/emp/pull/129#issuecomment-1349812325, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADSDCGFNFJZVLEWNYBBMILDWNDWCHANCNFSM6AAAAAAR366XGY . You are receiving this because you authored the 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 — Reply to this email directly, view it on GitHub https://github.com/biocore/emp/pull/129#issuecomment-1349821583, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADTZMU4RUVZN6UQU6AG7KTWNDWQLANCNFSM6AAAAAAR366XGY. You are receiving this because you were mentioned.