I'm trying to pick_de_novo_otus.py on 50 samples (.fa files) that I have trimmed and aligned (not using QIIME). It seemed straightforward, but I can't get the input format of the data right. I thought it could be comma delineated, but it says that the file doesn't exist 'home/Data/KK.01.fa,KK.02.fa,KK.03B.fa,KK.04.fa,KK.05.fa' (command below)
pick_de_novo_otus.py -i home/Data/KK.01.fa,KK.02.fa,KK.03B.fa,KK.04.fa,KK.05.fa -o home/Data/OTU&
I also tried using -i *.fa instead, but that gave the same result. When processing a large number of samples through the OTU picking, what is the proper way to input your files?