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Gibbons-Lab / aquaponics

Analysis code and scripts for the Aquaponics collab with Jessica Day et. al.
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Species of plant pathogens #12

Closed jessicaday closed 5 years ago

jessicaday commented 5 years ago

Do you think it's worth looking into the pseudomonas/serratia species that the reads are mapping to (despite the 10% error rate) so we can more closely examine species that are classified as plant pathogens already? I think Nitin/Sean might have mentioned this could be a good thing to explore. What do you think?

cdiener commented 5 years ago

I can only identify the following 3:

AB076858.1.1505 "Aeromonas hydrophila subsp. hydrophila"
AB506442.1.1535 "Rahnella sp. PCRCB18"                                 
AJ279052.1.1359 "Serratia sp. 1 MBK-v1"

However, there is big chance this just happens to be the closest species. You probably have something new here. I would only put confidence in A. hydrophila.

jessicaday commented 5 years ago

Strange since Rahnella is positively correlated with plant growth phenotypes...

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On Wed, Mar 13, 2019 at 8:20 PM Christian Diener notifications@github.com wrote:

I can only identify the following 3:

AB076858.1.1505 "Aeromonas hydrophila subsp. hydrophila" AB506442.1.1535 "Rahnella sp. PCRCB18" AJ279052.1.1359 "Serratia sp. 1 MBK-v1"

However, there is big chance this just happens to be the closest species. You probably have something new here. I would only put confidence in A. hydrophila.

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