About filtering the input biom file

[coralzhang]

Hi, I have a question about the input biom file.
Regarding the interpretation of the results, does it make more sense to include the OTU table that includes all the taxa, or include only the taxa at the same levels, say only taxa at the family or genus level? Another way to ask this question, if I input a biom file with or without the taxonomy of the otus, does it make a difference? Will songbird look at the taxonomy?
Many thanks!

[mortonjt]

No, songbird will not look at the taxonomy. If you want to collapse taxa, you'll want to do it yourself with the qiime taxa collapse command. https://docs.qiime2.org/2020.8/plugins/available/taxa/collapse/

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On Tue, Nov 24, 2020 at 7:11 PM coralzhang ***@***.***> wrote: Hi, I have a question about the input biom file. Regarding the interpretation of the results, does it make more sense to include the OTU table that includes all the taxa, or include only the taxa at the same levels, say only taxa at the family *or* genus level? Another way to ask this question, if I input a biom file with or without the taxonomy of the otus, does it make a difference? Will songbird look at the taxonomy? Many thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#145>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA75VXOJUMOEVBBBSD66OQDSRRRTPANCNFSM4UBWLWFA> .

[coralzhang]

So can I interpret your answer as- If I were to use the songbird standalone, then would you recommend inputting the biom file with OTU table at one selected level, say genus level, because otherwise, having taxa of different levels, say both the genus and family levels in the OTU table is violating the multinomial assumption, technically? Correct?

[mortonjt]

I wouldn't know how to use taxa at different levels, so I can't comment on this. Unless you are talking about having a custom script to aggregate taxa on the phylogenetic tree. If that is the case, that is totally fine, but songbird can't do only any of that - you'd need to feed in preprocessed biom tables yourself.

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On Tue, Nov 24, 2020 at 8:37 PM coralzhang ***@***.***> wrote: So can I interpret your answer as- If I were to use the songbird standalone, then would you recommend inputting the biom file with OTU table at one selected level, say genus level, because otherwise, having taxa of different levels, say both the genus and family levels in the OTU table is violating the multinomial assumption, technically? Correct? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#145 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA75VXLMA4PBYREGQVMJNZLSRR3XLANCNFSM4UBWLWFA> .

[coralzhang]

Thanks for the response and sorry about my ill-posed question.
Suppose I have a biom file with a OTU table that contains counts for 2 families and each family has 4 genera.
Would you suggest me to a) input the biom file with only 2 lines of the counts for the families only (or 8 lines of counts for the genera) or b) input a biom file with 10 lines of counts for families and genera together?

[mortonjt]

I'm having trouble understanding this question - it would help if you provided a snapshot of the table you are trying to analyze. Also, this doesn't seem to be a songbird question - I would recommend to follow up on the qiime2 forums, since the community there would be in a better position to answer this type of question.

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On Wed, Nov 25, 2020 at 11:53 AM coralzhang ***@***.***> wrote: Thanks for the response and sorry about my ill-posed question. Suppose I have a biom file with a OTU table that contains counts for 2 families and each family has 4 genera. Would you suggest me to a) input the biom file with only 2 lines of the counts for the families only (or 8 lines of counts for the genera) or b) input a biom file with 10 lines of counts for families and genera together? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#145 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA75VXOIHRIGFDG4ZAC76O3SRVHD5ANCNFSM4UBWLWFA> .