Dear Galaxy users that also use Megan,
I hope you can help me combining Galaxy with Megan4. I followed the Galaxy metagenome workflow (author aun1) on shotgun DNA 454 sequences of two samples that I would like to compare. The results are two nice trees and tables with the lowest taxonomic ranks for the two samples.
Besides the taxonomy I am also interested in the functions and I would like to use Megan4 (with SEED and KEGG classification) for this purpose. I tried to import a Galaxy file (.tabular) with c1 =high quality segment name and c2-c13 =blasthit results and a Galaxy fasta file with the high quality segment names and sequences. This does not work and I receive the message parsing failed, no reads found.
I am interested to know how you solved this issue and which files in the Galaxy metagenome workflow you use to import into Megan4.
Or maybe there is other software that you use to compare suits of functional genes in your metagenome datasets?
Judith van Bleijswijk