annotate SMART/galaxy/GetDifferentialExpression.xml @ 22:1e3f2c2657a3

Deleted selected files
author m-zytnicki
date Mon, 29 Apr 2013 03:26:07 -0400
parents 94ab73e8a190
children 0ab839023fe4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 <tool id="GetDifferentialExpression" name="get differential expression">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 <description>Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file.</description>
18
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
3 <requirements>
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
4 <requirement type="set_environment">PYTHONPATH</requirement>
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
5 </requirements>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 <command interpreter="python">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 ../Java/Python/GetDifferentialExpression.py -i $formatType.inputFileName1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 #if $formatType.FormatInputFileName1 == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 -f bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 #elif $formatType.FormatInputFileName1 == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 -f gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 #elif $formatType.FormatInputFileName1 == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 -f gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 #elif $formatType.FormatInputFileName1 == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 -f gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 #elif $formatType.FormatInputFileName1 == 'sam':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 -f sam
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 #elif $formatType.FormatInputFileName1 == 'gtf':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 -f gtf
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 -j $formatType2.inputFileName2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 #if $formatType2.FormatInputFileName2 == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 -g bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 #elif $formatType2.FormatInputFileName2 == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 -g gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 #elif $formatType2.FormatInputFileName2 == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 -g gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 #elif $formatType2.FormatInputFileName2 == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 -g gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 #elif $formatType2.FormatInputFileName2 == 'sam':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 -g sam
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 #elif $formatType2.FormatInputFileName2 == 'gtf':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 -g gtf
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 -k $formatTypeRef.inputFileNameRef
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 #if $formatTypeRef.FormatInputFileNameRef == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 -l bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 #elif $formatTypeRef.FormatInputFileNameRef == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 -l gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 #elif $formatTypeRef.FormatInputFileNameRef == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 -l gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 #elif $formatTypeRef.FormatInputFileNameRef == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 -l gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 #elif $formatTypeRef.FormatInputFileNameRef == 'sam':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 -l sam
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 #elif $formatTypeRef.FormatInputFileNameRef == 'gtf':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 -l gtf
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 -o $outputFileGff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 $simple
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 $adjusted
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 #if $optionSimplePara.simplePara == 'Yes':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 -S $optionSimplePara.paraValue
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 #if $optionFixedSizeFactor.FSF == 'Yes':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 -x $optionFixedSizeFactor.FSFValue
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65 #if $optionFDR.FDR == 'Yes':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 -d $optionFDR.FDRValue
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 </command>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 <inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 <conditional name="formatType">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
73 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
74 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
75 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
76 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
77 <option value="sam">sam</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
78 <option value="gtf">gtf</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
79 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
80 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
81 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
82 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
83 <when value="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
84 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
85 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
86 <when value="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
87 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
88 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
89 <when value="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
90 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
91 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
92 <when value="sam">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
93 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
94 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
95 <when value="gtf">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
96 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
97 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
98 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
99
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
100 <conditional name="formatType2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
101 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
102 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
103 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
104 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
105 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
106 <option value="sam">sam</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
107 <option value="gtf">gtf</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
108 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
109 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
110 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
111 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
112 <when value="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
113 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
114 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
115 <when value="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
116 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
117 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
118 <when value="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
119 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
120 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
121 <when value="sam">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
122 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
123 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
124 <when value="gtf">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
125 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
126 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
127 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
128
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
129 <conditional name="formatTypeRef">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
130 <param name="FormatInputFileNameRef" type="select" label="Input Ref File Format ">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
131 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
132 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
133 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
134 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
135 <option value="sam">sam</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
136 <option value="gtf">gtf</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
137 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
138 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
139 <param name="inputFileNameRef" format="bed" type="data" label="Input Ref File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
140 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
141 <when value="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
142 <param name="inputFileNameRef" format="gff" type="data" label="Input Ref File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
143 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
144 <when value="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
145 <param name="inputFileNameRef" format="gff2" type="data" label="Input Ref File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
146 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
147 <when value="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
148 <param name="inputFileNameRef" format="gff3" type="data" label="Input Ref File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
149 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
150 <when value="sam">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
151 <param name="inputFileNameRef" format="sam" type="data" label="Input Ref File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
152 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
153 <when value="gtf">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
154 <param name="inputFileNameRef" format="gtf" type="data" label="Input Ref File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
155 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
156 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
157
15
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
158 <param name="simple" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Normalize using the number of reads in each condition"/>
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
159 <param name="adjusted" type="boolean" truevalue="-a" falsevalue="" checked="false" label="Normalize using the number of reads of interquartile expression region"/>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
160
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
161 <conditional name="optionSimplePara">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
162 <param name="simplePara" type="select" label="provide the number of reads" >
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
163 <option value="Yes">Yes</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
164 <option value="No" selected="true">No</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
165 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
166 <when value="Yes">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
167 <param name="paraValue" type="text" value="None" label="provide the number of reads" />
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
168 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
169 <when value="No">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
170 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
171 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
172
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
173 <conditional name="optionFixedSizeFactor">
15
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
174 <param name="FSF" type="select" label="Give the magnification factor for the normalization using fixed size sliding windows in reference regions (leave empty for no such normalization)">
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
175 <option value="Yes">Yes</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
176 <option value="No" selected="true">No</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
177 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
178 <when value="Yes">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
179 <param name="FSFValue" type="integer" value="0" />
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
180 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
181 <when value="No">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
182 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
183 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
184
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
185 <conditional name="optionFDR">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
186 <param name="FDR" type="select" label="use FDR">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
187 <option value="Yes">Yes</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
188 <option value="No" selected="true">No</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
189 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
190 <when value="Yes">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
191 <param name="FDRValue" type="float" value="0.0"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
192 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
193 <when value="No">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
194 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
195 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
196
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
197 </inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
198
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
199 <outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
200 <data name="outputFileGff" format="gff3" label="[GetDifferentialExpression]out file"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
201 </outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
202
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
203 <help>
15
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
204 This tool compares two sets of data and find the differential expression. One very important component of the tool is the reference set. Actually, to use the tool, you need the two input sets of data, of course, and the reference set. The reference set is a set of genomic coordinates and, for each interval, it will count the number of feature on each sample and compute the differential expression. For each reference interval, it will output the direction of the regulation (up or down, with respect to the first input set), and a *p*-value from a Fisher exact test.
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
205
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
206 This reference set seems boring. Why not computing the differential expression without this set? The answer is: the differential expression of what? I cannot guess it. Actually, you might want to compare the expression of genes, of small RNAs, of transposable elements, of anything... So the reference set can be a list of genes, and in this case, you can compute the differential expression of genes. But you can also compute many other things.
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
207
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
208 Suppose that you cluster the data of your two input samples (you can do it with the *clusterize* and the *mergeTranscriptLists* tools). You now have a list of all the regions which are transcribed in at least one of the input samples. This can be your reference set. This reference set is interesting since you can detect the differential expression of data which is outside any annotation.
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
209
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
210 Suppose now that you clusterize using a sliding window the two input samples (you can do it with the *clusterizeBySlidingWindows* and the *mergeSlidingWindowsClusters* tools). You can now select all the regions of a given size which contain at least one read in one of the two input samples (do it with *selectByTag* and the tag **nbElements**). Again, this can be an other interesting reference set.
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
211
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
212 In most cases, the sizes of the two input samples will be different, so you should probably normalize the data, which is an available option. The ---rather crude--- normalization increases the number of data in the least populated sample and decreases the number of data in the most populated sample to the average number of data.
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
213 </help>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
214 </tool>