Hello! Im new in mothur and I’m wondering which is the best parameters (start and end) to use the screen.seqs command, since I lost around 80% of the sequences with the following criteria:
- screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, start=10368, end=25319, maxhomop=8)
It took 1192 secs to screen 1053264 sequences, removed 797534.
Its really bad to use this parameters? Im mean its valid to use the sequences as I did it or I will loose useful information?