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maracashay / DAWG-Helpline

Need help deciding what step to do or what specific commands to pass when analyzing your amplicon data? Ask AWAY! DAWG is here to help :)
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Picrust Prep .fna and .biom files #6

Open jspychalla opened 1 year ago

jspychalla commented 1 year ago

Hello, I don't know if this is still an active helpline since you graduated. I was following your YouTube picrust2 tutorial.

I have two problems with my file prep:

  1. My seqtab just has sequence names in the column. There is no ASV1, ASV2 etc before the sequence. The dataset in the video had ASV1; size = 0. The ; size = 0 needed to be removed in Excel to align later in picrust. How can I add to the column names of my Seqtab ASV 1 ASV2 without deleting the sequence after it? I think if I use colnames() in R it would just be replaced with ASV1 ASV2 etc.

  2. When I try to transfer my seqtab to get a biom file I run otu_t<- t(as(otu_table(seqtab))

I get the error message Error in h (simpleError(msg,call)): error in evaluating the argument 'x' in selecting a method for function 't': argument "taxa_are_rows" is mussing with no default

When I run

otu_t <- t(as(otu_table(seqtab), "matrix")) taxa_are_rows= FALSE

I get Error unexpected symbol in "otu_t <- t(as(otu_table(seqtab), "matrix")) taxa_are_rows= FALSE"

I try creating the biom file with my otu table not transferred and it looks all kinds of weird