Exporting #. of assigned reads as csv

Hi Daniel,

We are trying to export the number of assigned reads for particular taxon to csv format, however, it seems that the output is always summarized counts. We can visually see the assigned numbers in the GUI, which differs from the summarized. The problem comes during the export, the numbers doesn’t match.

Highlight taxon level we wish to export
File -> Export -> csv format -> taxonPath_to_count (also tried taxonName_to_count) -> assigned -> tab -> filename

I am not sure why this is so and it seems to happen for both MEGAN5 (v5.11.3) and MEGAN6 (v6.4) versions.

Kindly advise.

Thanks for your help!


If you request assigned counts, then MEGAN exports assigned counts, unless the node is collapsed, in which case the summarized count is exported. To avoid the latter, uncollapse any such node for which you don’t want this to kick in

Dear Daniel, I also have a question on this topic. in my original library the node that I am exporting there are sum=27355 and ass=12158, however when I open the extracted file (rma) it change to sum=12144 and ass=2571. if I export fast all the 27355 sequences are in the file? so what should I change to have all de 27355 sequences in the exported .rma file?

That doesn’t sound right
Can you give me more details?