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Locate fastq data associated with MGnify analyses #8

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s-meaden opened this issue Jun 21, 2022 · 0 comments
Open

Locate fastq data associated with MGnify analyses #8

s-meaden opened this issue Jun 21, 2022 · 0 comments

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@s-meaden
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s-meaden commented Jun 21, 2022

Adding this as an issue in case anyone has a similar problem.

MGnifyR::get_download_urls() doesn't return links for the read data (fastq) used to generate assemblies/analyses, but this may be useful for some scenarios.

A workaround is to run MGnifyR::mgnify_get_analyses_metadata() then use the ENA accessions returned under the sample_biosample column.

These accessions can be used with the enaGroupGet command from the enaBrowserTools scripts, e.g.:
enaGroupGet -f fastq SAMN04360062

Note that the enaDataGet throws an error and doesn't find the accession (for me at least).

Thanks @beadyallen for the package!

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