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updating runinfo CSV - #8
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planning to keep latest runinfo here on farm:
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so I am very confused about all of this 😆 - the runinfo file produced by the above contains the following headers:
but I also want these headers which come from ...somewhere else and are per-run. Working on it.
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ok, when sending to file select 'Run Info'. Doesn't work for whole thing but. |
this is useful: https://eaton-lab.org/articles/sra-downloads/ |
aaaaand maybe we should be using bigquery (or NCBI wants us to use it, whichever) - https://www.ncbi.nlm.nih.gov/sra/docs/sra-bigquery/ |
ok finally found my code for doing this on a sample by sample basis - https://github.com/dib-lab/2022-sra-gather/blob/main/summarize-sample.py run here: https://github.com/dib-lab/2022-sra-gather/blob/main/Snakefile |
the shell script at the bottom here: https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/74666-downloading-runinfo-table-from-sra-run-selector is useful |
search at https://www.ncbi.nlm.nih.gov/sra/ for "METAGENOMIC"[Source] NOT amplicon[All Fields]
direct link courtesy of luiz:
https://www.ncbi.nlm.nih.gov/sra/?term=%22METAGENOMIC%22%5BSource%5D%20NOT%20amplicon%5BAll%20Fields%5D
to download file:
send to... summary.
consider updating file https://osf.io/download/762mk/ referenced over at https://github.com/sourmash-bio/2022-search-sra-with-mastiff/blob/main/interpret-sra-live.ipynb
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