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? Regards, Judith van Bleijswijk
Hi Judith, The analysis in the paper focused on profiling taxonomic ranks. This was done with Megablast versus the GenBank databases NT & WGS. The accession identifiers being associated with nucleotide data, not protein (as would result from a comparison against NR), is most likely the problem. As I understand it, the Megan functional classification tools will want a protein identifier as input, but please confirm with the tool authors if the expected inputs are still not clear. BLAST+ tools are in the Main Galaxy Tool Shed and can be used with a local or cloud instance. http://getgalaxy.org http://toolshed.g2.bx.psu.edu Hopefully you have determined all of this by now, but just in case I wanted to send a reply to clarify, Take care, Jen Galaxy team On 7/18/12 3:26 AM, Judith van Bleijswijk wrote:
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?
Regards,
Judith van Bleijswijk
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Judith van Bleijswijk