Microbiome Helper

James, Sometimes opinions vary on whether to always reanalyze all together or to keep separate and

OK, first of all, let's look at your command you ran for the DADA2 step: qiime dada2 denoise-ccs

Yes, depending on your sample origins and community composition, you can have quite small numbers of

Thanks for you help Andre, I'll have a look and get back to you if need be. Best wishes, SK On

Okay, that makes alot more sense Andre, thanks for that. Cory On Tue, Jul 16, 2024 at 5:31 PM Andre

Hmm...I don't have that answer off the top of my head. Since it is related to PICRUSt2 and not

Hi Florine, For QIIME2 questions outside of the workflows and tutorials that we have on Microbiome

Hi Florine, You can find all older scripts in the release of Microbiome Helper v1.0 here. Please note

Hi caizhangbin, If you generated the "multi-sample-outfiles-w-m8.txt" in a Windows machine

this is the link for pipeline = https://github.com/LangilleLab/microbiome_helper/wiki/CBW%E2%80%

I am trying to transform a distance matrix from the qiime2 pathway using a centred log ratio in R. I

Hi! Thanks for your help, I was able to extract the distance-matrix.tsv file and transform it using R

Our trained classifiers are all here for individual download: http://kronos.pharmacology.dal.ca/

Bruce, Below I assume you meant to say you have thought about using the primer sequences to sort

I am using the code from the Random forest tutorial to analyze the microbiome data and even though I

These haven't been added currently because they're still in active development. We're

Yes, the link is in step 7 of the initial instructions to set up the environment and download the

OK I understand now the reasoning. Can you email me directly at my email below and I'll get the

The microbiome helper in conda does not include essential packages. 在2022年12月14日星期三 UTC+8 00:00:36

For the others on the group, Cory managed to find the solution to his problem: "I figured out

The wiki link/scripts you have listed below are for when you have run normal 16S analysis through

Hello, Has anyone been able to import picrust2 output files into R following the instruction on:

Okay, great- thanks for the quick reply! On Wednesday, August 3, 2022 at 2:27:08 PM UTC-5 André

Okay, that is what I figured, but wanted to confirm with someone more knowledgeable than myself. I

Hi, I am working through the MG SOPv3 with my own data and am at step 5.2 (Generate final normalized

Yes, you cannot have the same named cells at Level7 (or any level) for different genera at Level6 (ie

OK that size should be fine for overlapping then...some of your assembled sequences were way too long

The computer I'm using has 16 GB RAM, 6 cores and I allocated 4096 MB, 4 cores to the image in

Thank you so much! On Tuesday, March 15, 2022 at 2:14:05 PM UTC-7 André Comeau wrote: Yes, exactly.

Glad to hear it...and glad to hear feedback when things are working (and not)! We plan to eventually