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Welcome to the Microbiome Helper google group!
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S. Kose
,
Andre Comeau
7
May 13
VM box on website download link issue
Hmm...I don't have that answer off the top of my head. Since it is related to PICRUSt2 and not
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VM box on website download link issue
Hmm...I don't have that answer off the top of my head. Since it is related to PICRUSt2 and not
May 13
Florine Degrune
,
Robyn Wright
2
11/24/23
how to import already assembled trimmed reads in qiime2
Hi Florine, For QIIME2 questions outside of the workflows and tutorials that we have on Microbiome
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how to import already assembled trimmed reads in qiime2
Hi Florine, For QIIME2 questions outside of the workflows and tutorials that we have on Microbiome
11/24/23
Florine Degrune
,
Robyn Wright
4
11/24/23
cannot find qiime2_fastq_lengths.py
Hi Florine, You can find all older scripts in the release of Microbiome Helper v1.0 here. Please note
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cannot find qiime2_fastq_lengths.py
Hi Florine, You can find all older scripts in the release of Microbiome Helper v1.0 here. Please note
11/24/23
Z C
,
Dhwani Desai
2
9/27/23
"list index out of range" error
Hi caizhangbin, If you generated the "multi-sample-outfiles-w-m8.txt" in a Windows machine
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"list index out of range" error
Hi caizhangbin, If you generated the "multi-sample-outfiles-w-m8.txt" in a Windows machine
9/27/23
Mahesh Chinthalapudi
2
8/8/23
Script file for combine_merged_files.py
this is the link for pipeline = https://github.com/LangilleLab/microbiome_helper/wiki/CBW%E2%80%
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Script file for combine_merged_files.py
this is the link for pipeline = https://github.com/LangilleLab/microbiome_helper/wiki/CBW%E2%80%
8/8/23
Shannon Wallace
6/12/23
Trouble Applying a Centred Log Ratio on qiime2 Distance Matrix in R
I am trying to transform a distance matrix from the qiime2 pathway using a centred log ratio in R. I
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Trouble Applying a Centred Log Ratio on qiime2 Distance Matrix in R
I am trying to transform a distance matrix from the qiime2 pathway using a centred log ratio in R. I
6/12/23
Shannon Wallace
,
Andre Comeau
3
6/6/23
Can qiime be used to normalize data?
Hi! Thanks for your help, I was able to extract the distance-matrix.tsv file and transform it using R
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Can qiime be used to normalize data?
Hi! Thanks for your help, I was able to extract the distance-matrix.tsv file and transform it using R
6/6/23
mj
,
Andre Comeau
2
4/10/23
feature-classifier classify-sklearn job killed due to memory contraints
Our trained classifiers are all here for individual download: http://kronos.pharmacology.dal.ca/
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feature-classifier classify-sklearn job killed due to memory contraints
Our trained classifiers are all here for individual download: http://kronos.pharmacology.dal.ca/
4/10/23
eric nash
,
Andre Comeau
4
3/28/23
Extended index set
Bruce, Below I assume you meant to say you have thought about using the primer sequences to sort
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Extended index set
Bruce, Below I assume you meant to say you have thought about using the primer sequences to sort
3/28/23
Amruta Joshi
1/5/23
Random forest in R
I am using the code from the Random forest tutorial to analyze the microbiome data and even though I
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Random forest in R
I am using the code from the Random forest tutorial to analyze the microbiome data and even though I
1/5/23
Wang cs001632
,
Robyn Wright
2
12/14/22
Where is run_TaxonomyFunctionSearchMegan.pl for mmseqs2?
These haven't been added currently because they're still in active development. We're
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Where is run_TaxonomyFunctionSearchMegan.pl for mmseqs2?
These haven't been added currently because they're still in active development. We're
12/14/22
Wang cs001632
, …
Robyn Wright
5
12/14/22
Any tutorial contained a example data can be downloaded?
Yes, the link is in step 7 of the initial instructions to set up the environment and download the
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Any tutorial contained a example data can be downloaded?
Yes, the link is in step 7 of the initial instructions to set up the environment and download the
12/14/22
David Bars
,
Andre Comeau
4
12/13/22
Script run_contaminant_filter.pl
OK I understand now the reasoning. Can you email me directly at my email below and I'll get the
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Script run_contaminant_filter.pl
OK I understand now the reasoning. Can you email me directly at my email below and I'll get the
12/13/22
Wang cs001632
2
12/13/22
Is there a way to easily install microbiome helper in server?
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
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Is there a way to easily install microbiome helper in server?
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
12/13/22
Cory Bishop
,
Andre Comeau
2
10/18/22
/usr/bin/bash: seqtk: command not found
For the others on the group, Cory managed to find the solution to his problem: "I figured out
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/usr/bin/bash: seqtk: command not found
For the others on the group, Cory managed to find the solution to his problem: "I figured out
10/18/22
Md.Ishtiak Rashid
,
Andre Comeau
2
9/12/22
STAMP file preparation problem
The wiki link/scripts you have listed below are for when you have run normal 16S analysis through
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STAMP file preparation problem
The wiki link/scripts you have listed below are for when you have run normal 16S analysis through
9/12/22
Jewelna Akorli
8/18/22
Picrsut2 import to R
Hello, Has anyone been able to import picrust2 output files into R following the instruction on:
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Picrsut2 import to R
Hello, Has anyone been able to import picrust2 output files into R following the instruction on:
8/18/22
Rachel Mugge
,
Andre Comeau
3
8/3/22
Question about wet lab method: "small mean insert size" warning from metagenome assembly
Okay, great- thanks for the quick reply! On Wednesday, August 3, 2022 at 2:27:08 PM UTC-5 André
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Question about wet lab method: "small mean insert size" warning from metagenome assembly
Okay, great- thanks for the quick reply! On Wednesday, August 3, 2022 at 2:27:08 PM UTC-5 André
8/3/22
Rachel Mugge
,
Andre Comeau
16
7/28/22
Kraken2 returns majority (97%+) reads unclassified
Okay, that is what I figured, but wanted to confirm with someone more knowledgeable than myself. I
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Kraken2 returns majority (97%+) reads unclassified
Okay, that is what I figured, but wanted to confirm with someone more knowledgeable than myself. I
7/28/22
Rachel Mugge
7/24/22
Empty file produced from 'parse_Taxonomy_Function.py' script
Hi, I am working through the MG SOPv3 with my own data and am at step 5.2 (Generate final normalized
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Empty file produced from 'parse_Taxonomy_Function.py' script
Hi, I am working through the MG SOPv3 with my own data and am at step 5.2 (Generate final normalized
7/24/22
kkalya...@gmail.com
,
Andre Comeau
5
6/20/22
Input file for STAMP
Yes, you cannot have the same named cells at Level7 (or any level) for different genera at Level6 (ie
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Input file for STAMP
Yes, you cannot have the same named cells at Level7 (or any level) for different genera at Level6 (ie
6/20/22
Abdullahi Muhammad
,
Andre Comeau
5
3/22/22
Why do I loose 36.8% of reads while merging reads?
OK that size should be fine for overlapping then...some of your assembled sequences were way too long
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Why do I loose 36.8% of reads while merging reads?
OK that size should be fine for overlapping then...some of your assembled sequences were way too long
3/22/22
Mariem
,
Andre Comeau
5
3/21/22
Plug-in error
The computer I'm using has 16 GB RAM, 6 cores and I allocated 4096 MB, 4 cores to the image in
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Plug-in error
The computer I'm using has 16 GB RAM, 6 cores and I allocated 4096 MB, 4 cores to the image in
3/21/22
Brian Simison
,
Andre Comeau
4
3/16/22
determine mean read depth
Thank you so much! On Tuesday, March 15, 2022 at 2:14:05 PM UTC-7 André Comeau wrote: Yes, exactly.
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determine mean read depth
Thank you so much! On Tuesday, March 15, 2022 at 2:14:05 PM UTC-7 André Comeau wrote: Yes, exactly.
3/16/22
Lexie Blalock
,
Andre Comeau
2
2/9/22
Thanks for the PacBio CCS Amplicon SOP v1 (qiime2) workflow
Glad to hear it...and glad to hear feedback when things are working (and not)! We plan to eventually
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Thanks for the PacBio CCS Amplicon SOP v1 (qiime2) workflow
Glad to hear it...and glad to hear feedback when things are working (and not)! We plan to eventually
2/9/22
Alan Hudson
,
Gavin Douglas
2
1/25/22
Visualising PICRUSt2 output in Stamp
Sorry for missing your message on the PICRUSt2 google group - you can see my response here: https://
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Visualising PICRUSt2 output in Stamp
Sorry for missing your message on the PICRUSt2 google group - you can see my response here: https://
1/25/22
Leo FR
, …
Brian Simison
12
1/7/22
CATEGORY_METADATA
Thank you so much André ! Very helpful explanations. On Thursday, January 6, 2022 at 8:45:09 AM UTC-8
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CATEGORY_METADATA
Thank you so much André ! Very helpful explanations. On Thursday, January 6, 2022 at 8:45:09 AM UTC-8
1/7/22
Cory Bishop
,
Andre Comeau
5
8/26/21
memory error even with low rpb
Hmm...16 Gb might be OK for the SILVA ref dbase (note some of the QIIME2 forum answers are saying it
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memory error even with low rpb
Hmm...16 Gb might be OK for the SILVA ref dbase (note some of the QIIME2 forum answers are saying it
8/26/21
Cory Bishop
,
Andre Comeau
5
8/24/21
1.7 Import FASTQs as QIIME 2 artifact
OK - I tested on 2019.7 and so is working at least on that version (if not later ones). ANDRÉ M.
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1.7 Import FASTQs as QIIME 2 artifact
OK - I tested on 2019.7 and so is working at least on that version (if not later ones). ANDRÉ M.
8/24/21
ravi chandra
8/27/20
Help regarding starting with QIIME2 Virtual box and data analysis!
Hi All, I have installed QIIME2 vbox. I have a bunch of fast.q files to analyze. Could you please
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Help regarding starting with QIIME2 Virtual box and data analysis!
Hi All, I have installed QIIME2 vbox. I have a bunch of fast.q files to analyze. Could you please
8/27/20