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Analyze sequences from iSeq run 5/15/21 and 5/24/21 #13

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hollygene opened this issue Jun 10, 2021 · 1 comment

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hollygene commented Jun 10, 2021

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hollygene created this issue from a note in panCoV_Screen (In Progress)

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hollygene commented Jun 10, 2021

Goal: RdRp library

make sure to get wide margins
for diagnostics of sequences

Download sequences from BaseSpace:

unindexed reads > anything interesting?
what assembler for amplicons? > SPAdes
unindexed because robot messed up
equine CoV reference genome
de novo assemble first?
degenerate primers - in hopes of finding new viruses
quasi-species
does isolate mean culture in FIP? > no
serverity of clinical illness in FIP:
graded 1-3
also some cats with black-market remdesevir drug - FIP isolates

hollygene moved this from In Progress to Done in panCoV_Screen

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