screen-seqs: optimize minimum vs optimize end

Commands in mothur
1

HI Pat,

My colleague and I are trying to figure out how the commands optimize=minlength and optimize=end differ in screen.seqs.

here is an example:
screen.seqs(fasta=beard.trim.align, start=13858, optimize=minlength, criteria=85, processors=7)
screen.seqs(fasta=beard.trim.align, start=13858, optimize=end, criteria=85, processors=7)

So from what we understand, optimize=minlength will get rid of any sequences that end before 90% of the other sequences end. What does optimize=end do?

We pondered the wiki page for screen.seqs but have only confused ourselves more! Do you have an illustration of a bell curve with cutoff points that you could add to illustrate it?

Thank you,

Joyce

PS beard.trim.align was actually the filename! We were going to think of a funny filename to put up here and realized it was already pretty good :slight_smile:

2

The end parameter looks at the spot in the alignment, whereas the minlength deals with the number of bases in the sequence. So optimize=minlength will eliminate sequences that have less bases then 90% of the sequences, but optimize=end looks at the position in the alignment of the last base. So optimize=end will eliminate sequences whose last base is located before 90% of the sequences.

3

Thank you! That makes sense, I get it now :smiley: