MEGAN: Exported number of assigned reads is actually the summarized hits

Question

[William R]

Dear all,

I am using Megan (v5.10.6) and trying to export the number of assigned reads (i.e., the number of reads) to a taxa. I used both GUI and terminal to get the counts. However, the resulted file include the summarized (i.e., total number of hits to a taxon and its descendants) counts, rather than the assigned values. If I use the GUI and double-click on a node I can see both values and corroborate that the exported file has the summarized value. Does anyone know if this is a known problem or is not?

Thanks, Will

[mkulecka]

When exporting reads in GUI there should be a dialogue box which lets you chose which option you want. I think it doesn't show only when you export reads from profile but I'm not sure.

[William R]

Yes, when exporting reads in GUI the dialogue appears and I selected "assigned". However, the exported values are summarized counts. That's reason I am wondering if it is a known problem.

Answer 1

[daniel.huson]

I just tried this and got two different outputs, depending on whether I selected Summary or Assigned, the features appears to work as it should (MEGAN 5.11.2).

Please note that for a collapsed node (i.e., a node that has children, but they are not visible), MEGAN exports the summarized counts, even if you select "Assigned". This is intended. If you want the assigned counts for such a node, that make sure that the node is not collapsed, i.e. that its children are shown.