Question: Megan unable to assign taxonomical information
0
gravatar for stu111392
4.0 years ago by
stu11139230
Germany/Kiel
stu11139230 wrote:

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

alignment • 2.2k views
ADD COMMENTlink modified 3.9 years ago by Istvan Albert ♦♦ 79k • written 4.0 years ago by stu11139230
0
gravatar for Istvan Albert
4.0 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

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 ;-) 

ADD COMMENTlink written 4.0 years ago by Istvan Albert ♦♦ 79k
0
gravatar for stu111392
3.9 years ago by
stu11139230
Germany/Kiel
stu11139230 wrote:

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.

ADD COMMENTlink written 3.9 years ago by stu11139230

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

ADD REPLYlink written 3.9 years ago by Istvan Albert ♦♦ 79k

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.

ADD REPLYlink written 3.9 years ago by stu11139230
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2126 users visited in the last hour