Go Back   SEQanswers > Applications Forums > Metagenomics

Similar Threads
Thread Thread Starter Forum Replies Last Post
BLAST+ creating custom blast database and using blast+ filtering features deniz Bioinformatics 3 07-07-2019 08:04 AM
Mg-rast --> megan ewilbanks Metagenomics 5 12-06-2014 04:08 PM
MEGAN - how many BLAST hits to keep for each? camilaz Bioinformatics 3 07-08-2014 07:30 AM
Custom Blast database for MEGAN metagenomics OllyBolly Bioinformatics 2 12-19-2012 11:19 PM
Blast-like program to use with MEGAN? kga1978 Bioinformatics 3 11-30-2012 06:26 AM

Thread Tools
Old 03-19-2015, 03:15 AM   #1
Junior Member
Location: irelans

Join Date: Feb 2013
Posts: 2
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?
orlajos is offline   Reply With Quote
Old 04-27-2015, 09:29 PM   #2
Location: Australia

Join Date: Aug 2012
Posts: 11

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.
Polecat is offline   Reply With Quote
Old 07-06-2015, 02:42 AM   #3
Location: Germany

Join Date: Mar 2013
Posts: 43

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.
uloeber is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:32 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO