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  • iltisanni
    Member
    • Mar 2017
    • 21
    #1

    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, 09:41 PM.
    Tags: None
  • pbm13
    Junior Member
    • Jan 2013
    • 5
    #2
    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

    Comment

    • iltisanni
      Member
      • Mar 2017
      • 21
      #3
      OK thank you.

      I will try to find an answer there and if I get one I'll post it here aswell.

      Comment

      • iltisanni
        Member
        • Mar 2017
        • 21
        #4
        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…

        Comment

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