MEGAN - no reads found

Question

[emilyc]

Bonjour,

I'm not familiar with MEGAN. My issue is that when I import a blastx file (that appears to work) alongside a file with contigs in .fasta format (that it calls reads), it tells me that there are "no reads found". Any tips? I know it's difficult to address these issues with GUI programs as I don't have an command line output/input to show.

Thanks for any help you can suggest, Emily

version: Creator: MEGAN (version 5.11.3, built 21 Jan 2016)

[5heikki]

I suggest you read the manual. I used MEGAN a long time ago. From what I remember, I ditched it because the mapping files were ancient and there were no instructions on how to generate new files, and I think the author never replied to my emails either..

edit.

See here:

Auxiliary mapping files for taxon analysis: If the BLAST or other comparison files do not contain taxon names, but do contain GI numbers, then load the following mapping file to allow MEGAN to determine taxon names. The file has to be unzipped before it can be used: http://www-ab.informatik.uni-tuebingen.de/data/software/megan5/download/gi_taxid-March2015X.zip This indexed file maps 659 million GI accession numbers to taxon ids. It will work with both DNA and protein alignments. It is based on the files "gi_taxid_nucl.dmp.gz" and "gi_taxid_prot.dmp.gz" that are available from NCBI and was extended by parsing by treating all GI numbers that appear together in the header line of some sequence in the NR database as equivialent. Non-indexed NCBI files will not work with MEGAN.

That file is nearly 4 years old. Hits to sequences that were deposited after that file was created will not be recognized. How many percent of your hits are to such sequences? I'm willing to bet it's more than half..