annotate bamCompare.xml @ 20:69ff16ba27bd draft

Uploaded
author bgruening
date Mon, 03 Feb 2014 15:47:26 -0500
parents 5ea8782d650c
children f85c85597f95
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
1 <tool id="deeptools_bamCompare" name="bamCompare" version="1.0.3">
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
2 <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
3 <expand macro="requirements" />
10
135f3bae5c56 Uploaded
bgruening
parents: 9
diff changeset
4 <expand macro="stdio" />
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
5 <macros>
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
6 <token name="@BINARY@">bamCompare</token>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
7 <import>deepTools_macros.xml</import>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
8 </macros>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
9 <command>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
10 bamCompare
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
11
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
12 @THREADS@
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
13
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
14 --bamfile1 '$bamFile1'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
15 -bai1 '${bamFile1.metadata.bam_index}'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
16 --bamfile2 '$bamFile2'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
17 -bai2 '${bamFile2.metadata.bam_index}'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
18
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
19 --outFileName '$outFileName'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
20 --outFileFormat '$outFileFormat'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
21
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
22 --fragmentLength $fragmentLength
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
23 --binSize $binSize
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
24
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
25 #if $scaling.method == 'SES':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
26 --scaleFactorsMethod SES
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
27 --sampleLength $scaling.sampleLength
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
28 #elif $scaling.method == 'readCount':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
29 --scaleFactorsMethod readCount
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
30 #elif $scaling.method == 'own':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
31 --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2'
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
32 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
33
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
34 --ratio $comparison.type
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
35
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
36 #if $comparison.type=='subtract':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
37 #if $comparison.normalization.type=='rpkm':
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
38 --normalizeUsingRPKM
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
39 #elif $comparison.normalization.type=='1x':
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
40
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
41 #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
42 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
43 #else:
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
44 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
45 #end if
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
46
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
47 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
48 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
49
20
69ff16ba27bd Uploaded
bgruening
parents: 18
diff changeset
50 #if str($region).strip() != '':
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
51 --region 'region'
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
52 #end if
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
53
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
54 #if $advancedOpt.showAdvancedOpt == "yes":
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
55 #if $advancedOpt.smoothLength:
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
56 --smoothLength '$advancedOpt.smoothLength'
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
57 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
58
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
59 $advancedOpt.doNotExtendPairedEnds
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
60 $advancedOpt.ignoreDuplicates
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
61
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
62 #if $advancedOpt.minMappingQuality:
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
63 --minMappingQuality '$advancedOpt.minMappingQuality'
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
64 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
65
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
66 --missingDataAsZero $advancedOpt.missingDataAsZero
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
67
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
68 #if str($advancedOpt.ignoreForNormalization).strip() != '':
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
69 --ignoreForNormalization $advancedOpt.ignoreForNormalization
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
70 #end if
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
71
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
72 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
73
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
74 </command>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
75
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
76 <inputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
77 <param name="bamFile1" format="bam" type="data" label="Treatment BAM file"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
78 help="The BAM file must be sorted."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
79
9
c53a73b8eef9 Uploaded
bgruening
parents: 0
diff changeset
80 <param name="bamFile2" format="bam" type="data" label="BAM file"
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
81 help="The BAM file must be sorted."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
82
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
83 <param name="fragmentLength" type="integer" value="300" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
84 label="Length of the average fragment size"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
85 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
86
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
87 <param name="binSize" type="integer" value="50" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
88 label="Bin size in bp"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
89 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
90
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
91 <conditional name="scaling">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
92 <param name="method" type="select"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
93 label="Method to use for scaling the largest sample to the smallest">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
94 <option value="readCount" selected="true">read count</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
95 <option value="SES">signal extraction scaling (SES)</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
96 <option value="own">enter own scaling factors</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
97 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
98 <when value="SES">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
99 <param name="sampleLength" type="integer" value="1000" min="10"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
100 label="Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two BAM files "
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
101 help="The default is fine. Only change it if you know what you are doing" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
102 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
103 <when value="readCount" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
104 <when value="own">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
105 <param name="scaleFactor1" type="float" value="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
106 label="Scale factor for treatment"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
107
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
108 <param name="scaleFactor2" type="float" value="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
109 label="Scale factor for input"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
110 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
111 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
112
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
113 <conditional name="comparison">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
114 <param name="type" type="select"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
115 label="How to compare the two files">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
116 <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
117 <option value="ratio">compute the ratio of the number of reads</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
118 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
119 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
120 <when value="log2" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
121 <when value="ratio" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
122 <when value="subtract">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
123 <conditional name="normalization">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
124 <param name="type" type="select" label="Normalization method" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
125 <option value="1x">Normalize coverage to 1x</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
126 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
127 <option value="no">Do not normalize or scale</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
128 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
129 <when value="rpkm" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
130 <when value="no" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
131 <when value="1x">
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
132 <expand macro="effectiveGenomeSize" />
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
133 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
134 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
135 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
136 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
137
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
138 <param name="outFileFormat" type="select" label="Coverage file format">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
139 <option value="bigwig" selected="true">bigwig</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
140 <option value="bedgraph">bedgraph</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
141 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
142
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
143 <expand macro="region_limit_operation" />
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
144
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
145 <conditional name="advancedOpt">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
146 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
147 <option value="no" selected="true">no</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
148 <option value="yes">yes</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
149 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
150 <when value="no" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
151 <when value="yes">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
152
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
153 <param name="smoothLength" type="integer" value="1" optional="true" min="1"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
154 label="Smooth values using the following length (in bp)"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
155 help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
156
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
157 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
158 label="Do not extend paired ends"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
159 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
160
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
161 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
162 label="Ignore duplicates"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
163 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
164
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
165 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
166 label="Minimum mapping quality (e.g. BOWTIE2 measures)"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
167 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
168
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
169 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
170 label ="Treat missing data as zero"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
171 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
172
17
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
173 <param name="ignoreForNormalization" type="text" value="" size="50"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
174 label="regions that should be excluded for calculating the scaling factor"
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
175 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
ef65d6b68ccc Uploaded
bgruening
parents: 10
diff changeset
176
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
177 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
178 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
179
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
180 </inputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
181 <outputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
182 <data format="bigwig" name="outFileName">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
183 <change_format>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
184 <when input="outFileFormat" value="bigwig" format="bigwig" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
185 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
186 </change_format>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
187 </data>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
188 </outputs>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
189 <help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
190
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
191 **What it does**
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
192
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
193 This tool compares two BAM files based on the number of mapped reads. To
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
194 compare the BAM files, the genome is partitioned into bins of equal size,
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
195 the reads are counted for each bin and each BAM file and finally, a summarizing value is reported.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
196 This value can be the ratio of the number of reads per bin, the log2 of the ratio or the difference.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
197 This tool can normalize the number of reads on each BAM file using the SES method
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
198 proposed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3). Normalization based on read counts is also available. The
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
199 output is either a bedGraph or a bigWig file containing the bin location and
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
200 the resulting comparison values.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
201 If paired-end reads are present, the fragment
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
202 length reported in the BAM file is used by default.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
203
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
204
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
205 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
206
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
207
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
208 You can find more details in the `bamCompare wiki`_.
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
209
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
210 .. _bamCompare wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
211
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
212
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
213 **Output files**:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
214
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
215 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
216
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
217 -----
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
218
18
5ea8782d650c Uploaded
bgruening
parents: 17
diff changeset
219 @REFERENCES@
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
220
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
221 </help>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
222 </tool>