Option for screen.seqs command

1

Dear all,
Can anyone explain me in simple language what does this options will do in screen.seqs command:

optimize=maxlength, criteria=90

2

My understanding is that the optimize=maxlength option with criteria=90 would remove all sequences which are longer than 90% of the sequences.

3

Okay sir. Thanks a lot.

4

Thanks @amwalkero0o for helping out!

This option is really a vestige of analyzing 454 and Sanger data. If you’re using MiSeq data, it should be pretty straightforward to manually pick a start and end coordinate based on the median position, since the reads really should all start and end at the same point. Anything that starts after the start coordinate and anything that ends before the end coordinate can safely be tossed.

1 Like
5

Thanks a lot Dr. schloss.