Megan unable to assign taxonomical information

Question

[stu111392]

Hey everybody,

until now I got nearly everything to work but I'am stuck with Megan which of course has a GUI (what an irony). Over a long time I tried to load blast outputs, outputs from Diamond and today even an rma file generated with malt into Megan. This file was generated mapping reads from the illumina Sequencer against a Viral nr db with malt. But nothing is working. Whenever I load something the program is unable to assign at least a single read.

Why is this happening? I even downloaded the auxiliary mapping files for the taxon analysis as described. Has somebody an idea?

With kind regards,

Julian

Answer 1

[Istvan Albert]

You have to make sure that it can recognize the taxonomical information in the data. MEGAN does that by can recognize either a FASTA ID in the alignments but for that make sure to add the mapping file in one of the data loading tabs, or it can parse taxa names from the fasta header but there too it needs to be in a specific format.

I will agree that the tool has a slight usability issue here, it is very easy to load up a file without specifying the right taxonomical mapping file hence leading to useless output. Keep reading the manual ;-)

Answer 2

[stu111392]

The import of Blast output files works now if I add the GI-mapping file. Then Megan works perfectly. But if I want to import SAM files from Diamond the program is again unable to assign the reads even if I load the GI-mapping file. Is there something else I have to load to get the results out of my SAM file? I don't want functional analysis like KEEG or SEED. Just the taxonomic binning. And I looked into the manual but I have no idea what's missing now.

[Istvan Albert]

the problem is always the same ;-) the name of the sequences in the alignment file do not match the what the programs expects via its mapping

[stu111392]

Maybe to you it is clear what to do to get these sam files to work but for me it is still a mystery.

MEGAN can now parse files in SAM format [10]. Note, however, that SAM files usually do not
contain the names of the taxa associated with the reference sequences and so one must supply
suitable mapping files that map identifiers used for the reference sequences to NCBI taxa, KEGG,
COG and/or SEED identifiers, see below.

I get that I must provide a suitable mapping file as described above but I don't get what kind of file it has to be fot the taxonomic analysis.