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baymlab / wastewater_analysis

Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification
MIT License
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Metadata #1

Closed dfeistel3 closed 3 years ago

dfeistel3 commented 3 years ago

not related to code, but its a bit unclear where to get the metadata.tsv from for the preprocessing step. Any input on where this is located or how to download it from the GISAD site?

jbaaijens commented 3 years ago

Hi @dfeistel3, the metadata has to be downloaded from GISAID, together with the genome sequences. For GISAID you have to register before you are allowed to download the data, which is why I can't provide it here. I’ll make a note about this in the instructions.

jbaaijens commented 3 years ago

Once you've registered on GISAID, go to EpiCoV -> Downloads -> Download packages -> FASTA and metadata