Confusion between krona and sequence_taxa.txt

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Ligia Catallina Muñoz Arenas

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May 1, 2018, 11:51:38 PM5/1/18
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Hi, I finished my analysis (in all mode), but I don't understand the relationship between krona and the results of sequence_taxa.txt.
 I have four different ecosystem with 3 replicas, and I need obtain the average of this replicas with their respective standar deviation, and then compare with PCA edge, but I can't do it.

Even I did the PCA edge but the results are huge and not understandable.



I appreciate your help.

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Guillaume Jospin

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May 2, 2018, 8:33:31 AM5/2/18
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Ligia Catallina Muñoz Arenas

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May 2, 2018, 10:47:27 PM5/2/18
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Thanks, I had read the document, the document says: ".html files – visual output of the sequence_taxa.txt file using the Krona viewer" but for example in my krona, Acidobacteria have 8% with 11574 reads and my sequence_taxa.txt talks about probability mass and I want know what is the relationship between those documents.




I appreciate your help.


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Guillaume Jospin

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May 2, 2018, 10:59:55 PM5/2/18
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Oh I think it's the addition of all the probability mass that has been assigned to that node or lower.
So lets say 3 reads had 20%, 50% and 50% probability mass on the same taxon, then it should show 1.2 reads for that taxon.
It's not really the number of reads that were assigned to the taxon which is why the number isn't whole.



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