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Mapping between phylogenetic tree edge table and the placement post-traversal edge #31

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HollyKArnold opened this issue Dec 30, 2019 · 0 comments

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@HollyKArnold
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I have done the following experiment:

I have a reference tree which was generated from full length 16S rRNA sequences.
I took these long sequences that were used to build the reference tree and cut these 16S rRNA sequences into short 200 basepair long regions.
I then placed these 200 long basepair reads onto the reference tree. Now I'm trying to determine the distance from the placed read to the read that it was derived from.
To do this, I'm trying to map the edges in get.placements(p) to the edge table in jTree$edge:

j = read.jplace("epa_result.1100F.200.jplace")
jTree = get.tree(j)
jTree

p = get.placements(j, "best")
head(p)

how can I map between these two things?

jTree$edges
p$edge_num

Thanks so much for any help that you could provide

epa_result.1100F.200.jplace.txt
.

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