search

biocore / emp

Code repository of the Earth Microbiome Project.
http://www.earthmicrobiome.org
BSD 3-Clause "New" or "Revised" License
158 stars 68 forks source link

Availability of data for the multi-omics analyses on the EMP500 #133

Open S-Delattre opened 9 months ago

S-Delattre commented 9 months ago

Dear EMP community, I was wondering if the microbially-related metabolite feature table and Normalized microbe feature table were available for download (I am referring to the tables that were used to analyse differential metabolite-microbe co-occurrences as described in Extended Data Fig 1 of the Nature Microbiology paper). Recreating those tables from raw data seems possibles thanks to your extensive documentation but it would be time consuming. Best Simon

justinshaffer commented 9 months ago

Hi Simon,

Thanks for your note and interest in the EMP. We are currently still in the process of updating the EMP GitHub page to include all of the tables for the EMP500 analyses.

For now, one easy way to access the tables you are interested in is through QIITA: https://qiita.ucsd.edu/study/description/13114

If you do not already have a QIITA account, you can create one for free.

The metabolite table is here and has the ID: 120110 [image: Screenshot 2024-01-31 at 11.39.14 AM.png] The shotgun table is spread across four preps and you will have to merge one table from each prep to get the full table. The preps are under the 'Metagenomic' tab, and the following are the ones to merge tables from: [image: Screenshot 2024-02-01 at 8.24.00 AM.png] For each prep, select the 'per-genome predictions' table and add it to your analysis:

[image: Screenshot 2024-02-01 at 8.26.18 AM.png] ... and once you have all four added, create the analysis by clicking on the green button in the upper right-hand corner: [image: Screenshot 2024-02-01 at 8.27.35 AM.png] ... which will merge the four tables into one. You will need to perform subsequent filtering manually on this table, as this merged table will include all mapped sequences from all samples. You can do this in the analysis part of QIITA, or you can download the table and perform it externally.

Please let us know if you have any other questions.

Best wishes,

On Thu, Jan 25, 2024 at 10:43 AM S-Delattre @.***> wrote:

Dear EMP community, I was wondering if the microbially-related metabolite feature table and Normalized microbe feature table were available for download (I am referring to the tables that were used to analyse differential metabolite-microbe co-occurrences as described in Extended Data Fig 1 of the Nature Microbiology paper). Recreating those tables from raw data seems possibles thanks to your extensive documentation but it would be time consuming. Best Simon

— Reply to this email directly, view it on GitHub https://github.com/biocore/emp/issues/133, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADSDCGE4VGOOJ2KCQXXTMJ3YQKRVDAVCNFSM6AAAAABCK76GYWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYDAOJWG42DCMA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Justin Shaffer, PhD Assistant Professor Department of Biology College of Science and Mathematics California State University, Fresno justinshafferbio.wordpress.com

S-Delattre commented 6 months ago

Hi all, I have two questions, 1) regarding the metadata, I am interested in the environmental parameters such as salinity, ph. But theose values are missing in about 80% of the time in the table on QIITA. Is there another version of the table? 2) The metabolomics files are not on QIITA, I found the data using the instruction from the paper but the sample names do not match the convention for the file on QIITA, could you point me toward the metabolic result that I could cross reference with the 16S? Thanks

justinshaffer commented 5 months ago

Happy to help.

  1. Unfortunately, this information was not provided for the samples for which it is missing.
  2. The BIOM tables for the LC-MS/MS and GC-MS data are available on QIITA (study ID: 13114) and the sample IDs correspond to the other data layers (this is a requirement of QIITA). Can you please clarify the issue?