Choose mapping files: nucl_acc2tax with nucleotide references and prot_acc2tax with protein references

User Questions
1

Hi Daniel,
I started testing the Megan U trial with the blast file (.daa and .m8)
Now please help me rectify the problem.

  1. I used nucl_acc2tax-Nov2016.abin file for taxonomic mapping yet there was no taxonomic description done (see screenshot)
  2. Is pfam an inbuilt function as I could not find a mapping file for that on the download page, while putting the blast file there was an option for mapping file.
  3. KEGG and SEED had reads assigned to it but no sub classification was done in the result which is strange.(see screenshot)
  4. Please clarify on LCA parameters for the analysis(should it be left as it is)

Here are the parameter and mapping file I used

Taxonomy - nucl_acc2tax-Nov2016.abin
EGGNOG - acc2eggnog-Oct2016X.abin
INTERPRO2GO- acc2interpro-Nov2016XX.abin
KEGG - acc2kegg-Nov2016X-ue.abin
PFAM – “no file available on download page”
SEED - acc2seed-May2015XX.abin

here is screen shot with log file, taxonomy and KEGG window. Please help rectify the problem

megan.jpg1280×720 105 KB

2

For alignments against an NCBI protein reference database please use prot_acc2tax…
The file nucl_acc2tax is to be used with nucleotide references