using trump=. in filter.seqs()

Commands in mothur
1

Hi Everyone,
The output of my align.seqs() command looks like this:
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…T-------AC—GT-AG-GGT------------------------------------------------------------------------------------------

----------------------------------------------------------------------------------------------------------------------------------------------------------GCG
-A-G---------------------------------------------------------------------------------------------------------------------------------------------------------


Now when I am using filter.seqs() command with trump=. parameter I am getting only the names of the sequences in the filter.fasta file and no sequence. But without trump parameter I am getting filtered sequences. Could any one tell me why this is happening and what trump does? I thought it only removes '.' as that I provided.

Thanks!!!

2

Do you understand how filter.seqs(trump=.) works? Please see the filter.seqs page. You need to run screen.seqs, with the appropriate parameters, before running filter.seqs.