MEGAN annotation

[morning latte]

Hello experts,

I am using MEGAN to parse BLAST result and have a question regarding it. When I used the "inspect" function of MEGAN, all the contigs had identified taxonomic information to species level even though some of them (usually most of them) were only identified to family or genus level from tree view or exported DSV format. Does anyone have any idea why identified species information in not shown on the tree view or DSV file? Any advice would be greatly appreciated. Hope I am making myself clear.

[lorendarith]

I'm not sure I understood the situation, but maybe this will help.

I guess when you are referring to all contigs having identified taxonomic information to species level you are talking about the output of BLAST and then when you are saying that some or all of them were only identified to family or genus level it is an output of MEGAN. Am I right?
If so then it's maybe because of the LCA algorithm that MEGAN uses to assign hits to certain levels. There are options in MEGAN which define the criteria for hits being assigned to a certain level like minsupport and if the same BLAST query had several best hits in the database you used (among other MEGAN parameters to discard or keep reads). The default value for minsupport is [5] I think, which means you will only see species nodes in the tree which have at least 5 BLAST hits and all other (e.g.) species hits will be assigned to the higher node which is in this case genus.

I hope this makes sense and is what you are actually asking for, lol.

[morning latte]

Thanks for your clear explanation. This was really helpful.