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Assess the ability to detect viruses #6

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bhillmann opened this issue Nov 18, 2016 · 7 comments
Open
2 tasks done

Assess the ability to detect viruses #6

bhillmann opened this issue Nov 18, 2016 · 7 comments
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@RRShieldsCutler
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@bhillmann
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bhillmann commented Nov 18, 2016 •
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  • Assess virome recovery

  • Find out how deep you have to sequence human stool to get good recall of viruses (based on comparisons to deep shotgun)
@RRShieldsCutler RRShieldsCutler self-assigned this Nov 19, 2016
@RRShieldsCutler
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Sounds like we need a virome.ctr shogun database. There's gotta be a refseq virus set or something...

@bhillmann
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bhillmann commented Nov 21, 2016 •
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This is accessible for sure.

@bhillmann
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Can you give me write access to:

/project/flatiron2/ben/projects/analysis_SHOGUN/detect_viruses

@RRShieldsCutler
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Ok, you should have access now.

@bhillmann
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Can you rerun this with the confidence UTree version? Then we should be done.

@RRShieldsCutler
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Running currently. Should finish this evening sometime. I'll update with the result when it finishes.

@RRShieldsCutler
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Finished, results here:

/project/flatiron2/ben/projects/analysis_SHOGUN/detect_viruses/results/karlsson161205/shogun_utree_lca_out/

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@danknights @bhillmann @RRShieldsCutler