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Old 05-16-2018, 05:59 AM   #1
iltisanni
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Location: Mainz, Germany

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Default MEGAN - species summary

Hi,

for those who know the free (community) MEGAN software.

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
... ...

Does anyone know how to get that information from MEGAN... this software is really complex and confusing imho

Last edited by iltisanni; 05-16-2018 at 10:41 PM.
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Old 05-16-2018, 01:10 PM   #2
pbm13
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I have been trying to get similar info out of Megan. I do not know the answer but there is a MEGAN forum called MEGAN community, you might want to try posting there
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Old 05-16-2018, 10:38 PM   #3
iltisanni
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OK thank you.

I will try to find an answer there and if I get one I'll post it here aswell.
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Old 05-17-2018, 04:35 AM   #4
iltisanni
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Still no answer in the community forum but I think I found a workaround:


uncollapse all, select all leaves, list summary, copy everything into an editor, delete blank lines and replace : by \t -> paste into Excel…
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