Below is the beginning of a Blastn file produced by Malt that I import into Megan for a taxo assignment.
The species Curimata macrops was not present in my tre and map files that I used with MALT then the reads were therefore assigned to the Curimata genus level (tax | 143033).
Query = M03493: 133: 000000000-BMGCL: 1: 1101: 11332: 5072 1: N: 0: 1
Curimatá | tax | 143033 | macrops | ITAPE226-15 | COI-5P |
I manually added the Curimata macrops taxon to my MEGAN tre and map files:
(3000038 Curimata macrops -1 100)
How can I now inform Megan to assign the reads that contain in the headers of the Blastn file the term Curimata and macrops to taxon 3000038 (Curimata macrops).
This would allow for quick changes without having to redo the alignments with MALT.
when parsing the blastn file, provide MEGAN with a synonyms file for taxonomy assignment that contains a mapping of the word Curimata to taxon 3000038, tab separated:
MEGAN will then map anything match with the word Curimata in it to taxon 3000038
Let me know whether that works
I tested this synonym file. The problem is that I have other species of Curimata (other than macrops) that are then badly assigned.
I try the following :
It seems to work but it will not be the case if other genus have species that also have the name macrops.
So I tested the following synonym file:
Curimata|tax|143033| macrops 3000038
It does’nt work probably because space management is not possible.
An idea ?
I just took a look at this:
put the following line in your synonyms file:
tax | 143033 TAB 3000038
where TAB is a tab. Then MEGAN will use 3000038 when it finds the string “tax | 143033” (be sure to include the spaces). However, be sure that you have indeed added 3000038 to ncbi.tre and ncbi.map correctly. If there is a mistake here then the LCA algorithm will not compute the correct assignment/
Many thanks for your precious help.
I finally used the following string in the synonym file “tax | 143033 | macrops” which allows to reassign only macrops. This seems to work well.