How to get a species summary


#1

We sequenced a metagenome and now want to know what species with how many reads were found overall. If possible in a table like this:

species reads
Pseudomonas fluorescens 24000
Escherichia coli 16000
… …

We first used blastn to get all the species in our metagenome and are now importing the blast output to MEGAN.
Can anyone please help me out with that? I can’t find a way to get that kind of table although all information is available in seperate graphics…


#2

I think I found a workaround…
uncollapse all, select all leaves, list summary, copy everything and delete blank lines -> paste into Excel…


#3

use File->Export->Text Format


#4

Hello. I have a same problem. I ran Illumina for metagenomic analyses. However, I could not find out how to use MEGAN on the Illumina dataset. Can you provide hands-on exercise? I am pleased to visit Germany, for a few days.


#5

Please see:


#6

Ania,
Thank you very much for letting me know this relevant posting.

I will try to follow these procedures, which may take, for me, a few months (or more).

Keep in touch.