Remove.seqs

From mothur

The remove.seqs command takes a list of sequence names and either a fasta, name, group, list, 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.

Contents 1 Options 1.1 accnos option 1.2 fasta option 1.3 name option 1.4 group option 1.5 alignreport option 1.6 list option 1.7 taxonomy option 1.8 dups

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)

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

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
...

Note that remove.seqs will only remove the listed accession numbers, not the entire row of the .names file! This can lead to a mismatch between the number of sequences in a *.unique.fasta file and the number of rows in the corresponding *.names file. This can be problematic with some later commands, such as get.outrep.

To remove the entire line from the names file you must use the dups parameter. The dups parameter allows you to remove 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.

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

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 list 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);...

dups

The dups parameter may only be used in tandem with a namefile. By default dups=false, but if you set dups=true, then if any sequence in a specific line in the names 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.