I’m new to the forum, so I apologise if my question is duplicated.
I performed a 16S analysis of 192 samples following the available MiSeq SOP, but I made it separately for each sample instead of using the make.file command.
For this reason when I try to use the dist.seqs + cluster commands for OTU clustering the OTU numbers for each .fasta file are not correlative among samples.
Is there a way to merge all my filtered and aligned .fasta files keeping a sample codification in order to obtain an OTU table with the number of reads for each OTU for all samples?
I read about merge.files but I’m not sure if this command will create a groups file keeping codes for each sample…
Any help would be greatly appreciated.