remove.seqs

The remove.seqs command takes a list of sequence names and either a fastq, fasta, name, group, list, count or align.report file to generate a new file that does not contain the sequences in the list. This command may be used in conjunction with the list.seqs command to help screen a sequence collection. To complete this analysis, you need to download the folder compressed in the Esophagus.zip archive.

Options

To run remove.seqs, you must provide the accnos option and at least one other option. The command will generate a *.pick.* file.

accnos option

To generate an accnos file, let’s first run unique.seqs, summary.seqs, screen.seqs, and list.seqs:

mothur > unique.seqs(fasta=esophagus.fasta)

mothur > summary.seqs(fasta=esophagus.unique.fasta)

       Start   End NBases  Ambigs  Polymer
Minimum:   1   831 831 0   4
2.5%-tile: 1   841 841 0   4
25%-tile:  1   857 857 0   5
Median:    1   866 866 0   5
75%-tile:  1   870 870 0   5
97.5%-tile:    1   900 900 5   7
Maximum:   1   1378    1378    20  8
# of Seqs: 656

mothur > screen.seqs(fasta=esophagus.unique.fasta, maxambig=0)

This generates esophagus.unique.bad.accnos, a file with 129 sequences.

fasta option

To use the fasta option, follow this example:

mothur > remove.seqs(accnos=esophagus.unique.bad.accnos, fasta=esophagus.fasta)

This generates the file esophagus.pick.fasta, which contains the following lines:

>9_1_12
GCAAGTCGAGGGGAAAC...
>9_1_14
GCAAGTCGAGGGGAACG...
>9_1_15
GCAAGTCGAGGGGAAAC...
...

name option

To use the name option, follow this example:

mothur > remove.seqs(accnos=esophagus.unique.bad.accnos, name=esophagus.names)

This generates the file esophagus.pick.names, which contains the following lines:

65_5_22    65_5_22
65_5_12    65_5_12
59_7_23    59_7_23
59_7_7 59_7_7
65_5_28    65_5_28
65_9_13    65_9_13
9_6_11 9_6_11
...

By default, the entire line from a name file if you remove any name from the line. default=false. If dups=true, then remove.seqs outputs a new

.accnos file containing all the sequences removed. To turn this setting off, see the dups subsection, below.

dups

The dups parameter is only be used in tandem with a namefile. By default dups is set to true, which means that if any sequence in a specific line of the name file is in your .accnos file all sequences in that line will be removed. For example, let’s look at the following line from the esophagus.unique.good.accnos:

65_1_2 65_1_2,65_1_23,65_2_1,65_2_8

if dups=false, only 65_1_2 will be removed from your files, but if dups=true, then 65_1_2,65_1_23,65_2_1,65_2_8 will all be removed.

count option

The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information.

mothur > remove.seqs(accnos=esophagus.unique.bad.accnos, count=esophagus.count_table)

group option

To use the group option, follow this example:

mothur > remove.seqs(accnos=esophagus.unique.bad.accnos, group=esophagus.groups)

This generates the file esophagus.pick.groups, which contains the following lines:

9_1_12 B
9_1_14 B
9_1_15 B
9_1_16 B
9_1_18 B
...

alignreport option

To use the alignreport option, follow this example:

mothur > remove.seqs(accnos=esophagus.unique.bad.accnos, alignreport=esophagus.align.report)

This generates the file esophagus.pick.align.report, which contains the following lines:

QueryName  QueryLength TemplateName    TemplateLength  SearchMethod    SearchScore AlignmentMethod QueryStart  QueryEnd    TemplateStart   TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate  LongestInsert   SimBtwnQuery&Template   
9_1_12 866 108139  1525    kmer    62.17   needleman   1   866 50  917 868 2   0   0   91.36   
9_1_14 847 134265  1524    kmer    65.71   needleman   1   847 50  896 849 2   2   0   90.81   
9_1_15 866 108139  1525    kmer    61.47   needleman   1   866 50  917 869 3   1   1   91.02   
9_1_16 854 13820   1555    kmer    90.67   needleman   1   854 43  897 859 5   4   1   97.56   
...

list option

To use the list option, follow this example:

mothur > remove.seqs(accnos=esophagus.unique.bad.accnos, list=esophagus.fn.list)

This generates the file esophagus.fn.pick.list, which contains the following lines:

unique 480 9_6_14,9_1_12   9_1_14  9_1_15  9_1_16  9_1_18  9_1_19  9_1_20  9_1_26  9_1_27  ... 
0.00   265 9_4_14,9_7_28,9_1_26,9_6_14,9_1_12  9_2_20,9_1_14   9_1_15  9_1_16 ...
0.01   115 9_1_15,9_6_25,9_3_24,9_4_14,9_7_28,9_1_26,9_6_14,9_1_12 65_7_10,65_1_30,9_6_15,9_8_20, ...
...

taxonomy option

To use the taxonomy option, follow this example:

mothur > remove.seqs(accnos=esophagus.unique.bad.accnos, taxonomy=esophagus.silva.full.taxonomy)

This generates the file esophagus.silva.full.pick.taxonomy, which contains the following lines:

9_1_12 Bacteria(100);Bacteroidetes-Chlorobi(100);Bacteroidetes(100);Bacteroides-Prevotella(100);...
9_1_14 Bacteria(100);Bacteroidetes-Chlorobi(100);Bacteroidetes(100);Bacteroides-Prevotella(100);...
9_1_15 Bacteria(100);Bacteroidetes-Chlorobi(100);Bacteroidetes(100);Bacteroides-Prevotella(100);...
9_1_16 Bacteria(100);Firmicutes(100);Clostridia(100);Acidaminococcaceae(100);Veillonella(100);...

qfile option

The qfile option allows you to remove sequences from your quality file, and can be used as follows:

mothur > remove.seqs(accnos=esophagus.unique.good.accnos, qfile=esophagus.qual)

fastq option

The fastq option allows you to remove sequences from your fastq file.

mothur > remove.seqs(fastq=C10Fst.fastq, accnos=temp.accnos)

contigsreport

The contigsreport option allows you to select sequences from your contigsreport file.

Revisions

  • 1.28.0 Added count option
  • 1.33.0 Added fastq option
  • 1.37.0 Checks for repeat sequences names and eliminates them. Allows users creating their own templates to easily remove duplicate sequences from their reference files. #159
  • 1.40.0 - Allow for () characters in taxonomy definitions. #350
  • 1.44.0 - Adds contigsreport option. #660
  • 1.44.0 - Fixes bug with remove.seqs not removing empty groups from the count table. #675