subsampling fasta and taxonomy file

Can i use the classify sequence command to classify only a certain size in each sample (subsampaling)
because i have a different size of samples but i want to do the subsampling even before clustering into otu’s, i want to know what are the representative sequences but only for 4000 seqs in each of my sample

This is the orginal command for it:
classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table, reference=trainset9_032012.pds.fasta,, cutoff=80)

please help!!!

classify.seqs will classify anything you give it subsampled or not. but i’m not sure why you would subsample before classification. subsampling doesn’t affect classification and shouldn’t really affect the representative sequences.


Ok! thanks!