Show alignment and count number in MEGAN

User Questions
1

Hi there,

I am new to MEGAN and may have some basic questions to ask.
I have got the daa. files after blast my results with the CAZy database using DIAMOND. Then I Meganized the daa. files and mapped using the megan-map-Jan2021.db.zip. The results were successfully visualized on MEGAN. But I have two questions:

  1. how can I see the initial blast results?
    I understand that MEGAN transforms the initial blast results, but I lose some information of the initial results, saying, from the CAZy database, I could get the information of the total GH, GT families hits. But on MEGAN, I could only see the COG, SEED, EC, and taxo information. I tried to explore that using alignment options. I clicked on one node and show alignment, I saw the GH information. But, I don’t understand what does this number means? Is this the count number? I don’t feel they match the total count number? Please see the attached picture for this problem.

    MEGAN
    MEGAN897×313 93.4 KB

  2. I wondered how MEGAN calculates count numbers?
    Do they only calculate the presence/absence of a sequence to a reference database? what if the reference database has the same sequence under the different categories. I mean, for example, one enzyme could participate in different substrate utilization, when this enzyme corresponding coded sequence is present, all different substrate utilization categories will add 1 to the count?

Please let me know if I didn’t make the question sounds clear. Sincerely looking forward to you suggestions for those problems!

Best,
Minxi

2

The number behind an accession is the number of reads that have an alignment against the accession. Note that any given read aligns to several accessions simultaneously, and so the total of these counts will exceed the number of reads.