How to choose parameters for screen.seq command?

I am new to mothur and I don’t really understand a lot of stuff.
Right know I am confused how I must choose parameters (start, end, min/max-lenght, homop, ambig) for screen.seq command. Do I need to find answer from my previous commands like summary.seq? Or I just need to randomly select those numbers and look what works better, then how can I know that that specific option is the best one? Or there is even some constant numbers that all bioinformations use?

Thanks in advance for answer :slight_smile:

Hi there -

Definitely not random! :slight_smile: Where are you in the pipeline? If after aligning the sequences, look at the output of summary.seqs you’ll see the start and end columns in the table that is outputted. That should be a guide for what start and end positions to choose. You want to pick a start position at which most of your sequences start at or before. You want to pick an end position at which most of your sequences end at or after. Are you right after make.contigs? Then you 'll need to konw the typical length of sequences in your region and use a value for maxlength that is slightly more than that. You’ll always want an ambig value of 0 and you’ll be safe with a maxhomop of 10 or so. Are you using the V4 region of the gene? If so, your values should be pretty much what we have in the SOP.


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