Observation in the KEGG viewer

User Questions
1

Hi,
I opened a meganized .daa files in MEGAN, all reads have been assigned very well. But I have some questions.

  1. In the KEGG viewer, when I select a father node, I can only see the ‘Sum=balabala’. Is there any reads assigned to the father node?
  2. Can one read be assigned to different nodes in the KEGG viewer? I have summed reads of all child nodes and compare the sum with the number of reads annotated to their father node and I cannot find relationships between the two number.

Thanks a lot,

2

Reads are only assigned to leaves (KO nodes), so that is why there is no Ass=… on internal nodes.
Each read is only assigned to at most one KO, but the same KO can occur in many different places in the hierarchy, that is why the numbers in the tree can be larger than the number of reads.

3

Thanks for your fast reply and perfect explanation!
I have another question that in your paper ‘Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads’, how to know the number of reference gene sequences exist in a KEGG group in the synthetic community in Table 1?

4

Most of the genes were supposedly single copy genes, so we assumed the number is 1. But aligning the gene sequences against the genomes would also provide a count (I think that we did this)

5

@Daniel This may be obvious but I want to just want to make sure; I’m assuming the same counting mechanism you said applying to the KEGG viewer the OP was talking about also applies to the SEED viewer? Thus the reason for the difference in the numbers in the highlighted areas as seen in the attached pictures is due to simultaneous assignments? Thanks so much!

seed_viewer_differences
seed_viewer_differences.JPG1030×1018 146 KB

6

Yes, reads get counted multiple times in the hierarchy and so the number of assignments inferred on the hierarchy will usually be larger than the actual number of reads assigned.

7

Wonderful! Thanks so much for clearing that up!