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