mothur

Screen.seqs command

Hi there,
I used screen.seqs command with start-end values corresponding to 75%-title and I got removed more than a half of the sequences. I will apreciete to know if it´s normal to get removed this quantity of seqs or which is the best criteria I can follow to perform this comand.

Thanks

Hi there,

Those look like the right coordinates for the screen.seqs command. Could you maybe try using end=25318?. It does look like you have a decent number of sequences that were probably from non-specific amplification (e.g. things that start and end in the >43100 range). I’m not sure what this would be from - perhaps primer-dimer? What type of environment were you sequencing? Also, I wonder if your sequences still have the primers attached to be 300 nt long.

Pat