Filter Pqueries with low likelihood-to-weight ratio

[Alejandra Soto]

Hi all,

I get a .jplace file after my pplacer analysis and to visualize it I used iTOL. The problem is that some of the Pqueries (reads) have a really low likelihood-to-weight ratio and I was wondering if there is a way to filter and eliminate the reads that have a likelihood-to-weight ratio value below 0.5 and get a new .jplace file without them. I cannot find a command in guppy or pplacer that could help with this.

Thank you in advance,

Alejandra

[Erick Matsen]

I can't seem to find one either, but we designed the jplace format to be easy to read in using your favorite language and do such filtering yourself. Sorry not to be of more help!

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Frederick "Erick" Matsen, Associate Member
Fred Hutchinson Cancer Research Center
http://matsen.fredhutch.org/

[Alejandra Soto]

Thank you for the quick response! I am just trying to find a way to do what placeutil did on the old version of pplacer. I want to split up the placements based on EDPL or likelihood weight ratio. Also, I was wondering if there is a way to get a .jplace file that includes the EDPL values (besides the other information), I can just get a separate file with the name of the read and its EDPL value using the edpl command on guppy. I cannot find a way to do a manually filtering. I appreciate any help!