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

Commands in mothur
1

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):

LIB01.good.fasta
LIB01.bad.accnos
LIB01.good.count_table

Thanks

2

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.

3

Thanks,

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