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Meta-analysis of public nucleotide databases - help
Hey all,
I'm trying to start a meta-analysis for which I want to extract some 16S-based information from public databases. Moreover, I want to relate this information with any metadata found in the associated studies (everything from environmental variables to sequencing details).
For this, I realized some databases are available, like NCBI-Nucletotide, NCBI-SRA and EMBL-EBI-ENA, but I'm not sure about which one to use or whether I can use them all.
How can I filter only whole 16S sequences? Or even the most used 16S region?
One more thing would be how can I extract all the corresponding metadata?
Has anyone here tried this or anything similar before?
Thanks in advance!
André
I'm trying to start a meta-analysis for which I want to extract some 16S-based information from public databases. Moreover, I want to relate this information with any metadata found in the associated studies (everything from environmental variables to sequencing details).
For this, I realized some databases are available, like NCBI-Nucletotide, NCBI-SRA and EMBL-EBI-ENA, but I'm not sure about which one to use or whether I can use them all.
How can I filter only whole 16S sequences? Or even the most used 16S region?
One more thing would be how can I extract all the corresponding metadata?
Has anyone here tried this or anything similar before?
Thanks in advance!
André