Trim.seqs & screen.seqs in combination with .count_table

Dear users:

I used the following command;

mothur > trim.seqs(fasta=LIB01.fasta, maxambig=0, maxhomop=8, count=LIB01.count_table)

*the count_table contain the group information

Mothur (v 1.32.1) generated the following files:

Output File Names:

The trim fasta file contained the filtered sequences, while the scrap contained the “bad” sequences as we expected.

However the scrap.count_table file do not contain any information and the trim.count_table file do not contained any group information. In addition the trim.count_table file contained the seuences from the original fasta file.

If I used the following command: _mothur >screen.seqs(fasta=LIB01.fasta, maxambig=0, maxhomop=8, count=LIB01.count_table)_

the following output files contain the correct information (without scrap files):



Mothur does not create group information in the count table for trim.seqs unless you run it with an oligos file. As a workaround you could run the following,

mothur > trim.seqs(fasta=LIB01.fasta, maxambig=0, maxhomop=8)
mothur > list.seqs(fasta=current) - list seqeunce in trimmed fasta file
mothur > get.seqs(count=LIB01.count_table) selected those sequence from the count table

For the screen.seqs command, mothur does not output the scrap files.


Yes, that was my impression that you need the oligo file to modify the group information.

My approach was similar, but I used the scrap file (i.e. list) to remove ‘scrap’ sequences (mothur > remove.seqs) from the count_table file.

Thanks again