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
This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.