# Data resource **URL:** https://forum.biobakery.org/c/data-resource/33.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [About the Data resource category](https://forum.biobakery.org/t/about-the-data-resource-category/75)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 0
--- ## [External ID. Suffixes \_P and \_TR](https://forum.biobakery.org/t/external-id-suffixes-p-and-tr/9072)
**Author:** [@Diana\_MAGGESE](https://forum.biobakery.org/u/Diana_MAGGESE)\ **Replies:** 0\ **Last updated:** [September 30, 2026, 5:24pm UTC](https://forum.biobakery.org/t/external-id-suffixes-p-and-tr/9072 "2026-09-30T17:24:39Z")
Dear colleagues, I am Diana, and I am working with HMP2 data—specifically, the metagenomics data. My question is: what is the difference between samples with the suffixes \_TR and \_P and those without them? If I wanted t… --- ## [Issue with IBDMDB Omics and Metadata Download](https://forum.biobakery.org/t/issue-with-ibdmdb-omics-and-metadata-download/8970)
**Author:** [@JosephKatz](https://forum.biobakery.org/u/JosephKatz)\ **Replies:** 2\ **Last updated:** [June 22, 2026, 6:57pm UTC](https://forum.biobakery.org/t/issue-with-ibdmdb-omics-and-metadata-download/8970 "2026-06-22T18:57:22Z")
Hi, I am trying to download HMP2/IBDMDB metadata and omics product files from Results , but the downloads are failing across multiple networks. The metadata link points to: https://g-227ca.190ebd.75bc.data.globus.org/ib… --- ## [Issue with MTX taxonomic profiles](https://forum.biobakery.org/t/issue-with-mtx-taxonomic-profiles/8975)
**Author:** [@bioPpp](https://forum.biobakery.org/u/bioPpp)\ **Replies:** 0\ **Last updated:** [June 17, 2026, 6:02pm UTC](https://forum.biobakery.org/t/issue-with-mtx-taxonomic-profiles/8975 "2026-06-17T18:02:14Z")
Hello! Are taxonomic profiles for MTX available? If yes, where can I access them? Only found for the pilot study. Thank you! --- ## [Unable to download database](https://forum.biobakery.org/t/unable-to-download-database/8971)
**Author:** [@HLee](https://forum.biobakery.org/u/HLee)\ **Replies:** 0\ **Last updated:** [June 17, 2026, 9:55am UTC](https://forum.biobakery.org/t/unable-to-download-database/8971 "2026-06-17T09:55:13Z")
Hi, I cannot download IBDMDB databases from Results Please check whether the server is on. --- ## [License for Chocophlan?](https://forum.biobakery.org/t/license-for-chocophlan/8951)
**Author:** [@svalenzuela](https://forum.biobakery.org/u/svalenzuela)\ **Replies:** 0\ **Last updated:** [June 7, 2026, 8:53am UTC](https://forum.biobakery.org/t/license-for-chocophlan/8951 "2026-06-07T08:53:24Z")
Dears, We are building a public-facing SaaS for gut-microbiome analysis. Paying customers upload sequencing data; we run (along other pipelines) bioBakery tools server-side and return reports. We understand the bioBake… --- ## [Compare Metaphlan4 output with CuratedMetagenomicData?](https://forum.biobakery.org/t/compare-metaphlan4-output-with-curatedmetagenomicdata/5643)
**Author:** [@Minuzzi](https://forum.biobakery.org/u/Minuzzi)\ **Replies:** 4\ **Last updated:** [March 30, 2026, 9:59am UTC](https://forum.biobakery.org/t/compare-metaphlan4-output-with-curatedmetagenomicdata/5643 "2026-03-30T09:59:23Z")
Hello everyone, I am analysing some stool samples from a non-westernized population and I would like to compare my profile with that reported in the CuratedMetagenomicData dataset. I run metaphlan4 on my samples and ot… --- ## [Download via wget command is stopped](https://forum.biobakery.org/t/download-via-wget-command-is-stopped/8839)
**Author:** [@sooni](https://forum.biobakery.org/u/sooni)\ **Replies:** 1\ **Last updated:** [March 27, 2026, 9:51pm UTC](https://forum.biobakery.org/t/download-via-wget-command-is-stopped/8839 "2026-03-27T21:51:12Z")
I tried to download vJan25 from the MetaPhlAn4 database, but the download keeps stopping. The following is the code I ran and the result. wget -c http://cmprod1.cibio.unitn.it/biobakery4/metaphlan\_databases/mpa\_vJan25\_… --- ## [Gene annotation for IBDMDB Host Transcriptomics Data](https://forum.biobakery.org/t/gene-annotation-for-ibdmdb-host-transcriptomics-data/8842)
**Author:** [@ErikaKvalem](https://forum.biobakery.org/u/ErikaKvalem)\ **Replies:** 0\ **Last updated:** [March 27, 2026, 1:57pm UTC](https://forum.biobakery.org/t/gene-annotation-for-ibdmdb-host-transcriptomics-data/8842 "2026-03-27T13:57:07Z")
Dear BioBakery team, First of all, I would like to congratulate you on the IBDMDB project. We are currently analyzing IBDMDB host transcriptomics data and aim to transform the provided counts into TPM for deconvolution… --- ## [Reference tree downloading](https://forum.biobakery.org/t/reference-tree-downloading/8834)
**Author:** [@burdungy](https://forum.biobakery.org/u/burdungy)\ **Replies:** 5\ **Last updated:** [March 25, 2026, 9:34pm UTC](https://forum.biobakery.org/t/reference-tree-downloading/8834 "2026-03-25T21:34:21Z")
Hi, Previously, I downloaded a reference phylogenetic tree from https://github.com/biobakery/MetaPhlAn/blob/master/metaphlan/utils/mpa\_vJun23\_CHOCOPhlAnSGB\_202403.nwk. However, I can not find this kind of files in curre… --- ## [IBDMBD website unreachable](https://forum.biobakery.org/t/ibdmbd-website-unreachable/8829)
**Author:** [@yfgao](https://forum.biobakery.org/u/yfgao)\ **Replies:** 0\ **Last updated:** [March 17, 2026, 5:59am UTC](https://forum.biobakery.org/t/ibdmbd-website-unreachable/8829 "2026-03-17T05:59:38Z")
Hello, Recently, we noticed that the website (https://ibdmdb.org/) appears to be unreachable. We are in the middle of data analysis and it got cut off. We were wondering whether the site is temporarily down or if the da… --- ## [Appropriate input data selection for PICRUSt2 analysis](https://forum.biobakery.org/t/appropriate-input-data-selection-for-picrust2-analysis/8785)
**Author:** [@chen\_Ifrach](https://forum.biobakery.org/u/chen_Ifrach)\ **Replies:** 1\ **Last updated:** [March 2, 2026, 2:36pm UTC](https://forum.biobakery.org/t/appropriate-input-data-selection-for-picrust2-analysis/8785 "2026-03-02T14:36:30Z")
Hi, I am conducting a rat experiment in which I compare four different groups and look for differences among them. I sequenced the fecal microbiome using 16S rRNA, performed ANCOM analysis, and ran PICRUSt2. At the mom… --- ## [Issue with Data Download from IBDMDB](https://forum.biobakery.org/t/issue-with-data-download-from-ibdmdb/8731)
**Author:** [@jishuai](https://forum.biobakery.org/u/jishuai)\ **Replies:** 1\ **Last updated:** [January 23, 2026, 4:33pm UTC](https://forum.biobakery.org/t/issue-with-data-download-from-ibdmdb/8731 "2026-01-23T16:33:18Z")
Dear Support Team, I am experiencing difficulties downloading data from the IBDMDB website, specifically from the page: Results . The download consistently fails with an “ERR\_CONNECTION\_TIMED\_OUT” error. This issue has… --- ## [Biopsy 16S ASV sequences or paired-end raw data files](https://forum.biobakery.org/t/biopsy-16s-asv-sequences-or-paired-end-raw-data-files/8708)
**Author:** [@MaximilianBaumgartne](https://forum.biobakery.org/u/MaximilianBaumgartne)\ **Replies:** 0\ **Last updated:** [January 11, 2026, 11:34am UTC](https://forum.biobakery.org/t/biopsy-16s-asv-sequences-or-paired-end-raw-data-files/8708 "2026-01-11T11:34:31Z")
I’m interested in 16S from gut biopsies. To harmonize the data with my other datasets I would need to match ASV IDs to nucleotide sequences. Could you provide the matching table ? Alternatively I tried to re-run dada2 o… --- ## [How to match HTX samples with the closest MGX sampling in IBDMDB?](https://forum.biobakery.org/t/how-to-match-htx-samples-with-the-closest-mgx-sampling-in-ibdmdb/8624)
**Author:** [@daisakon1109](https://forum.biobakery.org/u/daisakon1109)\ **Replies:** 0\ **Last updated:** [November 17, 2025, 7:12pm UTC](https://forum.biobakery.org/t/how-to-match-htx-samples-with-the-closest-mgx-sampling-in-ibdmdb/8624 "2025-11-17T19:12:35Z")
Hello, I am currently trying to integrate host transcriptome (HTX) data with metagenomic (MGX) data from IBDMDB in order to analyze associations between host gene expression and the gut microbiome. To do this properly,… --- ## [Wgs files not complete?](https://forum.biobakery.org/t/wgs-files-not-complete/6332)
**Author:** [@chiaramazzoni](https://forum.biobakery.org/u/chiaramazzoni)\ **Replies:** 7\ **Last updated:** [September 29, 2025, 8:03am UTC](https://forum.biobakery.org/t/wgs-files-not-complete/6332 "2025-09-29T08:03:14Z")
Hi, I downloaded a number of wgs tar files, and I’m finding inconsistency between the number of reads in the fastq files and the number of reads stated in the metadata. I’m using bioawk to count the reads in the files … --- ## [When trying to download 'SwedishTwins\_metabolites.csv.gz' it says no such file](https://forum.biobakery.org/t/when-trying-to-download-swedishtwins-metabolites-csv-gz-it-says-no-such-file/8235)
**Author:** [@John1](https://forum.biobakery.org/u/John1)\ **Replies:** 1\ **Last updated:** [August 29, 2025, 3:35pm UTC](https://forum.biobakery.org/t/when-trying-to-download-swedishtwins-metabolites-csv-gz-it-says-no-such-file/8235 "2025-08-29T15:35:38Z")
Hello, I’m an MSc student in the University of Bristol (UK) and I am interested in doing a final year project on the interaction of gut bacteria and metabolites in the GI track and was looking to model it with a STGNN. I… --- ## [Structured Clinical Data in IBDMDB](https://forum.biobakery.org/t/structured-clinical-data-in-ibdmdb/8107)
**Author:** [@Ali\_Akeefe](https://forum.biobakery.org/u/Ali_Akeefe)\ **Replies:** 0\ **Last updated:** [June 4, 2025, 7:46pm UTC](https://forum.biobakery.org/t/structured-clinical-data-in-ibdmdb/8107 "2025-06-04T19:46:10Z")
Hello, I wanted to know what structured clinical data is in the IBDMDB dataset. I plan to make to develop and test a CPR using only your clinical data. Thanks! --- ## ["The page you are looking for is not found" Error](https://forum.biobakery.org/t/the-page-you-are-looking-for-is-not-found-error/7915)
**Author:** [@ellabakker](https://forum.biobakery.org/u/ellabakker)\ **Replies:** 8\ **Last updated:** [June 3, 2025, 12:05pm UTC](https://forum.biobakery.org/t/the-page-you-are-looking-for-is-not-found-error/7915 "2025-06-03T12:05:29Z")
There is an error on the IBD-MD database website. If you try to download any raw data, the following error is given: nginx error! The page you are looking for is not found. Something has triggered missing webpage on y… --- ## [Can not find several GGB numbers](https://forum.biobakery.org/t/can-not-find-several-ggb-numbers/8013)
**Author:** [@gb.uiuc](https://forum.biobakery.org/u/gb.uiuc)\ **Replies:** 0\ **Last updated:** [April 19, 2025, 5:03pm UTC](https://forum.biobakery.org/t/can-not-find-several-ggb-numbers/8013 "2025-04-19T17:03:27Z")
HI I am unable to figure out the genus name for few GGB number listed below. GGB34447 GGB37354 GGB64642 GGB44132 GGB49347 GGB49350 GGB52660 GGB56833 GGB63429 GGB89562 GGB89672 GGB89804 GGB90602 GGB90980 G… --- ## [LEfSe"\*\* tool (Galaxy Version 1.0)](https://forum.biobakery.org/t/lefse-tool-galaxy-version-1-0/7852)
**Author:** [@Khalid\_Ibrahim](https://forum.biobakery.org/u/Khalid_Ibrahim)\ **Replies:** 1\ **Last updated:** [March 13, 2025, 7:47pm UTC](https://forum.biobakery.org/t/lefse-tool-galaxy-version-1-0/7852 "2025-03-13T19:47:00Z")
I am attempting to use the “Format Data for LEfSe” tool (Galaxy Version 1.0) for my analysis. However, I am facing issues getting it to work properly. I even tried running the tool with the example dataset provided, such… --- ## [IBDMDB HMP2 host transcriptomics data](https://forum.biobakery.org/t/ibdmdb-hmp2-host-transcriptomics-data/7691)
**Author:** [@kestlermai](https://forum.biobakery.org/u/kestlermai)\ **Replies:** 0\ **Last updated:** [December 24, 2024, 1:40am UTC](https://forum.biobakery.org/t/ibdmdb-hmp2-host-transcriptomics-data/7691 "2024-12-24T01:40:55Z")
Dear Biobakery folks, I am currently analyzing host transcriptome data from the IBDMDB project, but I could not find detailed introductions to gene annotation files in either the IBDMDB project protocols page (https://ib… --- ## [IBDMDB HMP2 Pilot studies - data not available](https://forum.biobakery.org/t/ibdmdb-hmp2-pilot-studies-data-not-available/7382)
**Author:** [@Himali](https://forum.biobakery.org/u/Himali)\ **Replies:** 2\ **Last updated:** [November 18, 2024, 6:01pm UTC](https://forum.biobakery.org/t/ibdmdb-hmp2-pilot-studies-data-not-available/7382 "2024-11-18T18:01:01Z")
on IBDMDB the metadata suggests that there are 180 samples for stool\_16s but the but the product files in this link for this study only has 58 samples. Results Can you please urgently support on this topic and provide m… --- ## [Download MTX RAW data files](https://forum.biobakery.org/t/download-mtx-raw-data-files/7066)
**Author:** [@mariana](https://forum.biobakery.org/u/mariana)\ **Replies:** 1\ **Last updated:** [September 20, 2024, 3:27pm UTC](https://forum.biobakery.org/t/download-mtx-raw-data-files/7066 "2024-09-20T15:27:41Z")
Hello, I was wondering how can I download all the RAW datafiles from the HMP2 Metatranscriptomics. Thank you! --- ## [Matching 16S and Host Transcriptome Data for Biopsy Location](https://forum.biobakery.org/t/matching-16s-and-host-transcriptome-data-for-biopsy-location/7437)
**Author:** [@shreyanirmalan](https://forum.biobakery.org/u/shreyanirmalan)\ **Replies:** 0\ **Last updated:** [September 10, 2024, 9:31pm UTC](https://forum.biobakery.org/t/matching-16s-and-host-transcriptome-data-for-biopsy-location/7437 "2024-09-10T21:31:57Z")
Hello Biobakery team, I wanted to look at associations betewen the host transcriptome data and 16S data from the same biopsy location and wanted to know which column in the metadata table would ensure they are correctly… --- ## [Looking for Mycobacterium avium subsp. paratuberculosis](https://forum.biobakery.org/t/looking-for-mycobacterium-avium-subsp-paratuberculosis/7430)
**Author:** [@sherlock](https://forum.biobakery.org/u/sherlock)\ **Replies:** 0\ **Last updated:** [September 6, 2024, 1:32pm UTC](https://forum.biobakery.org/t/looking-for-mycobacterium-avium-subsp-paratuberculosis/7430 "2024-09-06T13:32:48Z")
Thank you for creating and sharing this wonderful dataset. I’d like to see if Mycobacterium avium subsp. paratuberculosis (MAP) is differentially present in the CD vs Healthy samples. I’ve been going through the datase… --- ## [Addition of new bacterial strain](https://forum.biobakery.org/t/addition-of-new-bacterial-strain/7385)
**Author:** [@Waqasuddin\_Khan](https://forum.biobakery.org/u/Waqasuddin_Khan)\ **Replies:** 0\ **Last updated:** [August 20, 2024, 6:23am UTC](https://forum.biobakery.org/t/addition-of-new-bacterial-strain/7385 "2024-08-20T06:23:25Z")
Dear bioBakery Community, Bifidobacterium infantis, a very important gut microbe of infants, is not added in the latest or even in any of the previous versions of the chocophlan. We request you to please add this bacte… --- ## [HMP2 metagenomics rawfiles](https://forum.biobakery.org/t/hmp2-metagenomics-rawfiles/7017)
**Author:** [@immunochem](https://forum.biobakery.org/u/immunochem)\ **Replies:** 1\ **Last updated:** [May 10, 2024, 3:42pm UTC](https://forum.biobakery.org/t/hmp2-metagenomics-rawfiles/7017 "2024-05-10T15:42:28Z")
Hello, I want to run HUManN3 with a custom databse on the raw files provided in the ibdmdb. From what I gather the raw files here have already been quality controlled and filtered with kneaddata. I’m a little confused b… --- ## [PiCrust 2.0 reference database genome list](https://forum.biobakery.org/t/picrust-2-0-reference-database-genome-list/7015)
**Author:** [@Rose06](https://forum.biobakery.org/u/Rose06)\ **Replies:** 0\ **Last updated:** [May 8, 2024, 10:48am UTC](https://forum.biobakery.org/t/picrust-2-0-reference-database-genome-list/7015 "2024-05-08T10:48:59Z")
Hello, I would like to know which genomes are included in the reference database of PiCrust 2.0, like which scientific strain/species names and taxonomy IDs. Is there any place where these can be found? Best, Rose --- ## [Virome Data Generated from IBDMDB](https://forum.biobakery.org/t/virome-data-generated-from-ibdmdb/6982)
**Author:** [@asinha23](https://forum.biobakery.org/u/asinha23)\ **Replies:** 0\ **Last updated:** [April 29, 2024, 7:47pm UTC](https://forum.biobakery.org/t/virome-data-generated-from-ibdmdb/6982 "2024-04-29T19:47:16Z")
Hi there, I was wondering about the viromics data included in the HMP2. Based on the available protocol, it is unclear to me if the resulting sequences would contain RNA or a mix of RNA and DNA viruses ? I know the MagM… [Next page](https://forum.biobakery.org/c/data-resource/33.md?page=1)