Mercurial > repos > lparsons > cutadapt

annotate cutadapt.xml @ 4:0a872e59164c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added discard_stderr_wrapper.sh script to catch report and redirect to stdout
author Lance Parsons <lparsons@princeton.edu>
date Wed, 25 May 2011 19:33:40 -0400
parents 7ed26fc9fa8a
children 1dada50cca8a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
7ed26fc9fa8a Updated for cutadapt 0.9.4, no longer need python wrapper
Lance Parsons <lparsons@princeton.edu>
parents: 2
diff changeset
1 <tool id="cutadapt" name="Remove adapter sequences" version="0.9.4">
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
2 <description>from high-throughput sequence data</description>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
3 <requirements>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
4 <requirement type="python-module">cutadapt</requirement>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
5 </requirements>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
6
4
0a872e59164c Added discard_stderr_wrapper.sh script to catch report and redirect to stdout
Lance Parsons <lparsons@princeton.edu>
parents: 3
diff changeset
7 <command interpreter="sh">discard_stderr_wrapper.sh cutadapt
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
8 #if $input.extension.startswith( "fastq"):
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
9 --format=fastq
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
10 #else
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
11 --format=$input.extension
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
12 #end if
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
13 #for $a in $adapters
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
14 -a '${a.adapter_source.adapter}'
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
15 #end for
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
16 #for $aa in $anywhere_adapters
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
17 -b '${aa.anywhere_adapter_source.anywhere_adapter}'
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
18 #end for
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
19 -e $error_rate
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
20 -n $count
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
21 -O $overlap
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
22 #if str($min) != '0':
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
23 -m $min
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
24 #end if
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
25 #if str($max) != '0':
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
26 -M $max
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
27 #end if
3
7ed26fc9fa8a Updated for cutadapt 0.9.4, no longer need python wrapper
Lance Parsons <lparsons@princeton.edu>
parents: 2
diff changeset
28 #if $discard:
7ed26fc9fa8a Updated for cutadapt 0.9.4, no longer need python wrapper
Lance Parsons <lparsons@princeton.edu>
parents: 2
diff changeset
29 --discard
7ed26fc9fa8a Updated for cutadapt 0.9.4, no longer need python wrapper
Lance Parsons <lparsons@princeton.edu>
parents: 2
diff changeset
30 #end if
7ed26fc9fa8a Updated for cutadapt 0.9.4, no longer need python wrapper
Lance Parsons <lparsons@princeton.edu>
parents: 2
diff changeset
31 '$input'
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
32 --output='$output'
4
0a872e59164c Added discard_stderr_wrapper.sh script to catch report and redirect to stdout
Lance Parsons <lparsons@princeton.edu>
parents: 3
diff changeset
33 > $report
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
34 </command>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
35 <inputs>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
36 <param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
37
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
38 <repeat name="adapters" title="3' Adapters">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
39 <conditional name="adapter_source">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
40 <param name="adapter_source_list" type="select" label="Source" >
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
41 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
42 <option value="user">Enter custom sequence</option>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
43 </param>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
44
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
45 <when value="user">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
46 <param name="adapter" size="30" label="Enter custom 3' adapter sequence" type="text" value="AATTGGCC" help="Sequence of an adapter that was ligated to the 3' end. The adapter itself and anything that follows is trimmed. If multiple adapters are specified, only the best matching adapter is trimmed."/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
47 </when>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
48
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
49 <when value="prebuilt">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
50 <param name="adapter" type="select" label="Choose 3' adapter" help="Sequence of an adapter that was ligated to the 3' end. The adapter itself and anything that follows is trimmed. If multiple adapters are specified, only the best matching adapter is trimmed.">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
51 <options from_file="fastx_clipper_sequences.txt">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
52 <column name="name" index="1"/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
53 <column name="value" index="0"/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
54 </options>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
55 </param>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
56 </when>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
57 </conditional>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
58 </repeat>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
59
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
60 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that was ligated to the 5' or 3' end. If the adapter is found within the read or overlapping the 3' end of the read, the behavior is the same as for the -a option. If the adapter overlaps the 5' end (beginning of the read), the initial portion of the read matching the adapter is trimmed, but anything that follows is kept. If multiple -a or -b options are given, only the best matching adapter is trimmed.">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
61 <conditional name="anywhere_adapter_source">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
62 <param name="anywhere_adapter_source_list" type="select" label="Source">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
63 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
64 <option value="user">Enter custom sequence</option>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
65 </param>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
66
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
67 <when value="user">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
68 <param name="anywhere_adapter" size="30" label="Enter custom 5' or 3' adapter sequence" type="text" value="AATTGGCC" help="Sequence of an adapter that was ligated to the 5' or 3' end. If the adapter is found within the read or overlapping the 3' end of the read, the behavior is the same as for the -a option. If the adapter overlaps the 5' end (beginning of the read), the initial portion of the read matching the adapter is trimmed, but anything that follows is kept. If multiple -a or -b options are given, only the best matching adapter is trimmed."/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
69 </when>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
70 <when value="prebuilt">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
71 <param name="anywhere_adapter" type="select" label="Choose 5' or 3' adapter" help="Sequence of an adapter that was ligated to the 5' or 3' end. If the adapter is found within the read or overlapping the 3' end of the read, the behavior is the same as for the -a option. If the adapter overlaps the 5' end (beginning of the read), the initial portion of the read matching the adapter is trimmed, but anything that follows is kept. If multiple -a or -b options are given, only the best matching adapter is trimmed.">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
72 <options from_file="fastx_clipper_sequences.txt">
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
73 <column name="name" index="1"/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
74 <column name="value" index="0"/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
75 </options>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
76 </param>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
77 </when>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
78 </conditional>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
79 </repeat>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
80
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
81 <param name="error_rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
82 <param name="count" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
83 <param name="overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified." />
3
7ed26fc9fa8a Updated for cutadapt 0.9.4, no longer need python wrapper
Lance Parsons <lparsons@princeton.edu>
parents: 2
diff changeset
84 <param name="discard" type="boolean" checked="False" default="False" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
85 <param name="min" type="integer" min="0" optional="true" value="0" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no minimum length." />
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
86 <param name="max" type="integer" min="0" optional="true" value="0" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no maximum length." />
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
87 </inputs>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
88 <outputs>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
89 <data format="txt" name="report" label="${tool.name} on ${on_string} (Report)" />
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
90 <data format="input" name="output" metadata_source="input"/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
91 </outputs>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
92
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
93 <tests>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
94 <test>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
95 <param name="input" value="fa_gc_content_input.fa"/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
96 <output name="out_file1" file="fa_gc_content_output.txt"/>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
97 </test>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
98 </tests>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
99
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
100 <help>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
101 This tool removes adapter sequences from DNA high-throughput
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
102 sequencing data. This is usually necessary when the read length of the
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
103 machine is longer than the molecule that is sequenced, such as in
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
104 microRNA data.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
105
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
106 The tool is based on the opensource cutadapt_ tool.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
107
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
108 -----
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
109
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
110 **Algorithm**
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
111
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
112 cutadapt uses a simple semi-global alignment algorithm, without any special optimizations.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
113 For speed, the algorithm is implemented as a Python extension module in calignmodule.c.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
114
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
115
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
116 **Partial adapter matches**
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
117
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
118 Cutadapt correctly deals with partial adapter matches. As an example, suppose
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
119 your adapter sequence is "ADAPTER" (specified via 3' Adapters parameter).
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
120 If you have these input sequences:
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
121
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
122 ::
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
123
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
124 MYSEQUENCEADAPTER
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
125 MYSEQUENCEADAP
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
126 MYSEQUENCEADAPTERSOMETHINGELSE
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
127
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
128 All of them will be trimmed to "MYSEQUENCE". If the sequence starts with an
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
129 adapter, like this:
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
130
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
131 ::
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
132
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
133 ADAPTERSOMETHING
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
134
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
135 It will be empty after trimming.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
136
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
137 When the allowed error rate is sufficiently high, errors in
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
138 the adapter sequence are allowed. For example, ADABTER (1 mismatch), ADAPTR (1 deletion),
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
139 and ADAPPTER (1 insertion) will all be recognized if the error rate is set to 0.15.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
140
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
141
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
142 **Allowing adapters anywhere**
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
143
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
144 Cutadapt assumes that any adapter specified via the *3` Adapters* parameter
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
145 was ligated to the 3' end of the sequence. This is the correct assumption for
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
146 at least the SOLiD and Illumina small RNA protocols and probably others.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
147
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
148 If, on the other hand, your adapter can also be ligated to the 5' end (on
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
149 purpose or by accident), you should tell cutadapt so by using the *5' or 3' (Anywhere)
2
f6b94b76d16b Update help
Lance Parsons <lparsons@princeton.edu>
parents: 0
diff changeset
150 Adapters* parameter. It will then use a different alignment algorithm and
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
151 correctly trim adapters that appear in the beginning of a read. An adapter
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
152 specified this way will also be found if it appears only partially in the
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
153 beginning of a read. For example, these sequences
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
154
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
155 ::
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
156
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
157 ADAPTERMYSEQUENCE
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
158 PTERMYSEQUENCE
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
159
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
160 will be trimmed to "MYSEQUENCE". Note that the regular algorithm would trim
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
161 the first read to an empty sequence.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
162
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
163 This parameter currently does not work with color space data.
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
164
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
165
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
166 .. _cutadapt: http://code.google.com/p/cutadapt/
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
167 </help>
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
168
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
169 </tool>