# Data resource **URL:** https://forum.biobakery.org/c/data-resource/33.md?page=3 [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) **Page:** 4 --- ## [EC details iHMP\_metabolomics](https://forum.biobakery.org/t/ec-details-ihmp-metabolomics/1178)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 2\ **Last updated:** [October 26, 2020, 1:48pm UTC](https://forum.biobakery.org/t/ec-details-ihmp-metabolomics/1178 "2020-10-26T13:48:02Z")
We are planning to use metabolomics and metagenomics data from the IBD dataset in our project. I have downloaded the metabolomic file named as “iHMP\_metabolomics” from the link /products/HMP2/MBX and the metagenomic fil… --- ## [Bad link to download core-genes](https://forum.biobakery.org/t/bad-link-to-download-core-genes/1098)
**Author:** [@MADscientist314](https://forum.biobakery.org/u/MADscientist314)\ **Replies:** 0\ **Last updated:** [September 30, 2020, 6:20pm UTC](https://forum.biobakery.org/t/bad-link-to-download-core-genes/1098 "2020-09-30T18:20:13Z")
I’m trying to download the identifiers of core genes that the system identified for all clades can be downloaded \[here\] but am getting a 404 error. --- ## [HMP2 path abundance matrix](https://forum.biobakery.org/t/hmp2-path-abundance-matrix/1006)
**Author:** [@Marco](https://forum.biobakery.org/u/Marco)\ **Replies:** 0\ **Last updated:** [September 11, 2020, 6:08pm UTC](https://forum.biobakery.org/t/hmp2-path-abundance-matrix/1006 "2020-09-11T18:08:22Z")
Hi all, we are a bioinformatics research group of the University of Padua. We are interested in carrying out analyzes on wgs data in patients with inflammatory bowel disease. Following your research we have downloaded H… --- ## [Speed up humann3](https://forum.biobakery.org/t/speed-up-humann3/640)
**Author:** [@Robin\_Mjelle](https://forum.biobakery.org/u/Robin_Mjelle)\ **Replies:** 1\ **Last updated:** [June 26, 2020, 7:08pm UTC](https://forum.biobakery.org/t/speed-up-humann3/640 "2020-06-26T19:08:42Z")
I am running a 77G input file into humann. It takes about a day to complete the analysis. Is there a way to speed up the process? I am only interested in identifying species og genera. This is my command: humann --thre… --- ## [dbGAP SRA samples](https://forum.biobakery.org/t/dbgap-sra-samples/123)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 3\ **Last updated:** [June 26, 2020, 1:10pm UTC](https://forum.biobakery.org/t/dbgap-sra-samples/123 "2020-06-26T13:10:19Z")
From: jgadeav@ibmcp.upv.es We are trying to download the raw data of the human RNAseq described in your paper, We got the GEO IDs, but there is no link to SRA. We can not acces to those raw data from ibdmdp neither. Cou… --- ## [UC patients data](https://forum.biobakery.org/t/uc-patients-data/481)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 3\ **Last updated:** [June 19, 2020, 5:12pm UTC](https://forum.biobakery.org/t/uc-patients-data/481 "2020-06-19T17:12:06Z")
We are interested in the host transcriptome data and the bacterial data (both 16S and metagenomics) in the presence of inflammation. Our focus is the inflammatory state in UC patients undergoing total proctocolectomy and… --- ## [Fasta sequences for metagenomic data](https://forum.biobakery.org/t/fasta-sequences-for-metagenomic-data/402)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 4\ **Last updated:** [May 26, 2020, 3:44pm UTC](https://forum.biobakery.org/t/fasta-sequences-for-metagenomic-data/402 "2020-05-26T15:44:40Z")
From: Alan.Cartmell@liverpool.ac.uk I am a Tenure-Track research fellow at Liverpool university with a current research interest in carbohydrate sulfatases found in the human gut microbiota. I recently read your paper i… --- ## [16S raw data adaptors / primers](https://forum.biobakery.org/t/16s-raw-data-adaptors-primers/416)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 1\ **Last updated:** [May 7, 2020, 7:43pm UTC](https://forum.biobakery.org/t/16s-raw-data-adaptors-primers/416 "2020-05-07T19:43:24Z")
I’m wondering if the 16S raw datafiles have had adaptors and primers trimmed? --- ## [Diversity data from HMP paper (The Human Microbiome Project Consortium 2012 Nature 486 207)](https://forum.biobakery.org/t/diversity-data-from-hmp-paper-the-human-microbiome-project-consortium-2012-nature-486-207/434)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 1\ **Last updated:** [May 5, 2020, 3:11pm UTC](https://forum.biobakery.org/t/diversity-data-from-hmp-paper-the-human-microbiome-project-consortium-2012-nature-486-207/434 "2020-05-05T15:11:09Z")
I am a microbial ecologist at the University of Warwick in the UK, working with veterinary epidemiologists to investigate chronic animal diseases, such as mastitis in cows and other ruminants. We are close to finishing a… --- ## [Dropbox link to hmp2\_analysis](https://forum.biobakery.org/t/dropbox-link-to-hmp2-analysis/420)
**Author:** [@ravinpoudel](https://forum.biobakery.org/u/ravinpoudel)\ **Replies:** 0\ **Last updated:** [May 1, 2020, 5:17pm UTC](https://forum.biobakery.org/t/dropbox-link-to-hmp2-analysis/420 "2020-05-01T17:17:40Z")
I have trying to reproduce the analyses as done in “Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases” following the code as deposited at the following repo. https://bitbucket.org/biobakery/hmp2\_… --- ## [Nature 569 (2019)](https://forum.biobakery.org/t/nature-569-2019/345)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 0\ **Last updated:** [April 15, 2020, 4:10pm UTC](https://forum.biobakery.org/t/nature-569-2019/345 "2020-04-15T16:10:35Z")
I try to analyze some additional files available, too. And especially I am curious on the coding found in one of them. Namely, in the file entitled „C18n\_NN” (https://ibdmdb.org/tunnel/public/HMP2/Metabolites/1723/rawfil… --- ## [Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases](https://forum.biobakery.org/t/multi-omics-of-the-gut-microbial-ecosystem-in-inflammatory-bowel-diseases/135)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 1\ **Last updated:** [April 10, 2020, 1:28pm UTC](https://forum.biobakery.org/t/multi-omics-of-the-gut-microbial-ecosystem-in-inflammatory-bowel-diseases/135 "2020-04-10T13:28:12Z")
From: 15011270109@163.com Dear Huttenhower professor: As mentioned in your article,your groups followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activi… --- ## [IBDMDB sample details](https://forum.biobakery.org/t/ibdmdb-sample-details/189)
**Author:** [@dpbisme](https://forum.biobakery.org/u/dpbisme)\ **Replies:** 2\ **Last updated:** [April 8, 2020, 9:51pm UTC](https://forum.biobakery.org/t/ibdmdb-sample-details/189 "2020-04-08T21:51:32Z")
Hi Sagun and Curtis - How many samples from the IBDMDB have 16S data available? I downloaded the sample details available on the iHMP site and filtered on ‘biopsy\_16S’ and ‘stool\_16S’ which returns 358 samples. However… --- ## [Request for information -- Dynamics of metatranscription in the inflammatory bowel disease gut microbiome](https://forum.biobakery.org/t/request-for-information-dynamics-of-metatranscription-in-the-inflammatory-bowel-disease-gut-microbiome/143)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 1\ **Last updated:** [January 15, 2020, 7:25pm UTC](https://forum.biobakery.org/t/request-for-information-dynamics-of-metatranscription-in-the-inflammatory-bowel-disease-gut-microbiome/143 "2020-01-15T19:25:06Z")
From: Phil Strandwitz \ Dear Dr. Huttenhower, I read through your excellent paper titled " Dynamics of metatranscription in the inflammatory bowel disease gut microbiome ", published in Nature,… --- ## [HMP shotgun metagenomic data request](https://forum.biobakery.org/t/hmp-shotgun-metagenomic-data-request/117)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 1\ **Last updated:** [January 2, 2020, 9:43pm UTC](https://forum.biobakery.org/t/hmp-shotgun-metagenomic-data-request/117 "2020-01-02T21:43:52Z")
From: Wu, Jiqiu \ I’m a master student in Imperial College London, and my theis is to study the role of CRISPRs in the dynamics of the infants gut microbiota. My results show that CRISPRs increas… [Previous page](https://forum.biobakery.org/c/data-resource/33.md?page=2)