sub.sample - question about "size" and "persample"

Commands in mothur
1

Good day!
I am working with sequences created in MiSeq SOP by make.contigs command.
For my data I would like to make smaller FASTA and group files with 10,000 reads per each barcode using:

sub.sample(fasta=xxxx.trim.contigs.fasta, group=xxxx.contigs.groups, size=10000, persample=true)
I am a little pazelled with “size” and “persample” options. Is the command line above correct?

Another question. Several barcodes are having read counts below 10K. How “sub.sample” treats “<10K” cases?

  1. collect all available reads to the new file
  2. reject the entire group

Thank you in advance!

2

sub.sample(fasta=xxxx.trim.contigs.fasta, group=xxxx.contigs.groups, size=10000, persample=true)
I am a little pazelled with “size” and “persample” options. Is the command line above correct?

That should work to get you 10000 sequences per group.

Several barcodes are having read counts below 10K. How “sub.sample” treats “<10K” cases?

It will reject the entire group.