Hi,
Can someone explain me the edges in red knowing that edges in yellow correspond to RBNH (orthogroup)? (this is a result from Orthofinder_graph.txt for one orthogroup (a), considering an inflation of 1.1, and which is split into two differents orthogroups (b) after clusterisation with an inflation of 1.5.
(a) : {AT1G29760, AT2G34380, MELO3C007187, OS09G36360, POTRI.011G072200, GSVIVG01014151001, GSVIVG01021275001, Solyc02g071900.2, Solyc07g062230.2}
(b): {GSVIVG01014151001, Solyc07g062230.2} & {Solyc02g071900.2, GSVIVG01021275001, AT1G29760, AT2G34380, MELO3C007187, OS09G36360, POTRI.011G072200}
Considering that,
q is connected to h in the orthogroup graph if B'qh > B'qR where R is an RBNH of q
these edges should not exist, no?
Thanks in advance
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It seems that the author of orthofinder does not suggest changing the inflation index. link
Hi Sishuo Wang,
I just think there is a mistake in the construction of the graph that could potentially impact the formed orthogroups. So I'm wondering if there is something I'm missing...
edit: the construction of the graph is independent of the inflation parameter.