mothur

Generate list file from OTU table

Dear all,

Thank you for the amazing resource! I was wondering whether there is a command in mothur to generate a list file (a classic mothur list file to use with classify.otu) from an OTU table generated using usearch? Usearch otutab output files do include a tab-separated text file which maps reads to OTUs (one read per line), but in a completely different format then the list file in mothur.

Best regards,

Sam

if you’re using a names file, I think you can reverse engineer a list from a shared and names file. I vaguely recall having a one liner that does that but I’d have to dig. If you have a count table rather than a names file, I dont’ think you can make the list.

Thank you for your answer! Since I did not generate OTUs in mothur, I also don’t have a names file. Mothur format output options when generating OTUs with usearch only include a shared file. Is generating OTUs in mothur the only way to go about this?

sorry I didn’t read closely to see that you have a otu like file. I think you can make.table from your output then make.shared but @wescott likely needs to weigh in

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