I’m currently using MEGAN 6.7.0, and I am working with 3-string .csv files of some metabarcoding data, (so I am providing the program with read names, BLAST matches and bitscores).
I think the LCA algorithm is returning good results, (they seem biologically reasonable), and I am able to export the number of reads assigned to each taxon from the program.
What I would like now to export is a file showing which reads were assigned to which taxa.
The options Export -> Reads and Export -> Matches are grayed out for me, (even when all the tree is selected).
I would like to export something like “TaxonName_to_Read”, but that option does not appear in my list of options for Export -> CSV Format.
Here is a small sample of my data:
Contig 483,GBVU419713|Austrostipa_sp._CHSL2012|rbcL|JQ933232,420.31 Contig 483,GRASS67607|Hesperostipa_comata|rbcL,420.31 Contig 483,GRASS67607|Hesperostipa_comata|rbcLa,420.31 Contig 483,GRASS74407|Achnatherum_hymenoides|rbcLa,420.31 Contig 483,GRASS74407|Achnatherum_hymenoides|rbcL,420.31 Contig 483,T19_Ausostipa_sp_rbcL,420.31 Contig 470,SDH118614|Medicago_polymorpha|ITS2,422.156 Contig 470,SDH338915|Medicago_polymorpha|ITS2,422.156 Contig 274,TDEF00812|Acacia_holosericea|rbcL,420.31 Contig 274,GBVW92913|Acacia_suma|rbcL|JX195516,420.31 Contig 274,GBVU199013|Inga_stipularis|rbcL|JQ626223,420.31 Contig 274,TDEF00112|Acacia_auriculiformis|rbcL,420.31
After the LCA algorithm has run and the tree has been created, I would like to export a file with the results of the LCA for each read, something like:
Contig 483,Poaceae Contig 470,Medicago Contig 274,Mimosidae
Any help with this would be greatly appreciated.