Greetings, I’m a student and I’m currently trying to use humann3.9 with the metaphlan4.1 output but I’m a little bit stuck cause with both the biom and the sam the humann gives me only UNMAPPED. I know that there is also the possibility to use the humann with fastq but i need to maintain the two programs separated. The thing i wanna ask is, what is the optimal metaphlan output to give to the humann?
Thank you for your patience and have a nice week.
If you’re running MetaPhlAn outside of HUMAnN, then you need to pass the default taxonomic profile MetaPhlAn creates to HUMAnN via the --taxonomic-profile flag. HUMAnN will also need the input reads used to generate that profile as its own --input. The taxonomic profile will be functioning as a guide in this case for putting together a relevant pangenome database to map the reads against.
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