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?
- collect all available reads to the new file
- reject the entire group
Thank you in advance!