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Old 03-19-2015, 03:15 AM   #1
orlajos
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Location: irelans

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Default MEGAN and blast against NR

I am hoping someone else has encountered this issue:
We have shotgun metagenomic samples which we have blasted against nr ( downloaded dec 2014); when we import the blast output onto MEGAN it all looks fine at the top taxonomical level.
However when we try to look at KEGG or COG we get zero reads assigned; this happens even when I load the Auxiliary mapping files for KEGG analysis as suggested on the MEGAN website. ( at the Load GI mapping tab on the KEGG tab)


Am I missing something completely obvious?
Orla
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Old 04-27-2015, 09:29 PM   #2
Polecat
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I had that issue. I had only asked for the best hit. The LCA analysis in MEGAN requires a minimum of 5 best hits to work.
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Old 07-06-2015, 02:42 AM   #3
uloeber
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I have the same issue. But setting Min Support to 5 doesn't fix the problem. Is that the parameter you meant? Would be great if anybody could help...
I performed a blastx to swissprot db without any evalues and outfmt 7. The import of the blast table doesn't seem to cause any problem.

Last edited by uloeber; 07-06-2015 at 02:44 AM.
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