Hi!
My partner and I are looking for a new project to do, and we are willing to help out with locating public datasets associated with:
Human Gut
Water
Soil
If anyone can help thank you in advance!
-Loraye Smith and Nwanneka Udolisa
How fun! Here are some suggestions for cool papers/datasets for you to explore.
- Wetland Soil - Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires - PubMed. You can get sequencing data for this project PRJNA1119519 here https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA1119519 for example, sample SRR29366187.
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2. Surface Water from Herschel Island, Canada. You can get sequencing data for this project PRJEB66156 here HER19_HER22_metaG_and_16Samplicons (ID 1109094) - BioProject - NCBI for example, sample ERR12120030.
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- Clinical gut/fecal microbiome Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data - PMC. You can get sequencing data for this project PRJNA754443 here PRJNA754443 - SRA - NCBI 1 for example, sample SRR15489009.
Thank you Valerie for the response! Do you know how I would upload my selected sequences from what you sent me in Galaxy?
-Loraye Smith
To upload your selected sequences in Galaxy:
In Galaxy Tools, use Download and Extract Reads in FASTQ format from NCBI SRA.
In Tool Parameters Select input type: ‘SRR accession’ and under Accession enter your SRR or ERR accession IDs of interest (e.g. SRR29366187). You can Select output format ‘gzip compressed fastq’ (but ‘uncompressed fastq’ is also OK if the files are not too large).