Rarefaction analysis of MetaPhlan output file

Hi community!!! This is my first post and I am very new in this field and naive with MEGAN.
I am analysing already submitted shotgun WGS metagenome sequence data with MetaPhlAn software. Can anyone please tell me if I can use MEGAN for rarefaction analysis of the shotgun sequence data?
If yes, then when I have to do the analysis-

1.prior to MetaPhlAn run? or,
2.after the bowtie2 step of MetaPhlAn? or,
3.after the profiling step of MetaPhlAn?

Thanks and regards,
DC7

Hi,

I think now it would be possible to generate a biom file in MetaPhlan using “–biom_output_file”, then you can import this biom file into MEGAN and make a rarefaction analysis.

Good luck
Mohamed

1 Like

Thanks @msabrysarhan for your response. Should I merge them before importing into MEGAN or should I import them individually? If I have to merge, I don’t find any tool to merge them!!!

Thanks,
DC7

I’m not sure whether this would be a straight forward process. Maybe you can try “qiime::merge_otu_tables.py” to merge your biom output files (http://qiime.org/scripts/merge_otu_tables.html).

Or,

you can use the new MetaPhlan option to merge the MetaPhlan output table (https://bitbucket.org/nsegata/metaphlan/src/ecf86f2c2a19d0f9c129963e2fb422e3ec33f965/utils/merge_metaphlan_tables.py), but then I don’t know if MetaPhlan supports combined table conversion or not!

Good luck
Mohamed

1 Like

Thanks… earlier I saw your first option. But, before running qiime::merge_otu_tables.py, the biom formats from (json) should be changed to qiime compatible format (hdf5).
Do you know how to do that?

Thanks,
DC7

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