Mercurial > repos > bgruening > deeptools_multi_bam_summary
annotate multiBamSummary.xml @ 28:004aea905d4d draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5
author | bgruening |
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date | Fri, 19 May 2023 08:32:23 +0000 |
parents | 0c8638172059 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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1 <tool id="deeptools_multi_bam_summary" name="multiBamSummary" version="@WRAPPER_VERSION@.0"> |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
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2 <description>calculates average read coverages for a list of two or more BAM/CRAM files</description> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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3 <macros> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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4 <token name="@BINARY@">multiBamSummary</token> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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5 <import>deepTools_macros.xml</import> |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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6 </macros> |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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7 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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8 <command> |
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9 <![CDATA[ |
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10 #set files=[] |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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11 #set labels=[] |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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12 |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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13 @multiple_input_bams@ |
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14 @BINARY@ |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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15 $mode.modeOpt |
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16 @THREADS@ |
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17 |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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18 --outFileName '$outFile' |
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19 --bamfiles #echo " ".join($files)# |
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20 --labels #echo " ".join($labels)# |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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21 |
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22 #if $outRawCounts: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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23 --outRawCounts '$outFileRawCounts' |
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24 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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25 |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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26 #if $scalingFactors: |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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27 --scalingFactors '$scalingFactorsFile' |
0c8638172059
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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28 #end if |
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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
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29 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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30 #if $mode.modeOpt == "bins": |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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31 --binSize '$mode.binSize' |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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32 --distanceBetweenBins '$mode.distanceBetweenBins' |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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33 #else: |
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34 --BED $mode.region_file |
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35 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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36 |
04b612e24e62
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37 #if str($region).strip() != '': |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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38 --region '$region' |
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39 #end if |
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40 |
04b612e24e62
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41 #if $advancedOpt.showAdvancedOpt == "yes": |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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42 @ADVANCED_OPTS_READ_PROCESSING@ |
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43 @ADVANCED_OPTS_GTF@ |
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44 @blacklist@ |
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45 #end if |
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46 ]]> |
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47 </command> |
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48 |
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49 <inputs> |
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50 <expand macro="multiple_input_bams" MIN="2"/> |
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51 <expand macro="custom_sample_labels" /> |
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52 |
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53 <conditional name="mode"> |
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54 <param name="modeOpt" type="select" label="Choose computation mode" |
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55 help="In the bins mode, the coverage is computed for equally |
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56 sized bins. \nIn BED file mode, a list of genomic regions |
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57 in BED or INTERVAL format has to be given. For each region |
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58 in the BED file, the number of overlapping reads from each BAM file is counted. |
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59 "> |
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60 <option value="bins" selected="true">Bins</option> |
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61 <option value="BED-file">Limit calculation to certain regions (BED file)</option> |
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62 </param> |
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63 <when value="bins"> |
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64 <param name="binSize" type="integer" value="10000" min="1" |
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65 label="Bin size in bp" |
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66 help="Length in bases of the window used to sample the genome. (--binSize)"/> |
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67 |
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68 <expand macro="distanceBetweenBins" /> |
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69 |
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70 </when> |
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71 <when value="BED-file"> |
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72 <param name="region_file" type="data" format="bed,gtf" |
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73 label="Region file in BED or INTERVAL format" |
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74 help="Coverage is computed for the number of reads that overlap such regions."/> |
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75 </when> |
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76 </conditional> |
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77 |
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78 <expand macro="region_limit_operation" /> |
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79 |
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80 <expand macro="advancedOpt_scaffold"> |
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81 <expand macro="read_processing_options" /> |
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82 <expand macro="gtf_options" /> |
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83 <expand macro="blacklist" /> |
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84 </expand> |
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85 |
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86 <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to file" help=""/> |
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87 <param argument="--scalingFactors" type="boolean" label="Save scaling factors" help="Scaling factors calculated as in DESeq2 and made directly compatible with bamCoverage."/> |
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88 |
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89 </inputs> |
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90 <outputs> |
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91 <data format="deeptools_coverage_matrix" name="outFile" label="${tool.name} on ${on_string}: correlation matrix" /> |
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92 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> |
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93 <filter>outRawCounts is True</filter> |
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94 </data> |
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95 <data format="tabular" name="scalingFactorsFile" label="${tool.name} on ${on_string}: scaling factors"> |
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96 <filter>scalingFactors is True</filter> |
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97 </data> |
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98 </outputs> |
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99 <tests> |
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100 <test> |
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101 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> |
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102 <param name="modeOpt" value="bins" /> |
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103 <param name="binSize" value="10" /> |
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104 <output name="outFile" file="multiBamSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> |
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105 </test> |
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106 <test> |
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107 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" /> |
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108 <param name="modeOpt" value="BED-file" /> |
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109 <param name="region_file" value="multiBamSummary_regions.bed" /> |
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110 <output name="outFile" file="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" /> |
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111 </test> |
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112 |
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113 |
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114 </tests> |
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115 <help> |
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116 <![CDATA[ |
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117 |
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118 What it does |
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119 ------------- |
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120 |
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121 This tool generates a matrix of read coverages for a list of genomic regions and at least two samples (BAM files). |
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122 The genome is split into bins of the given size. For each bin, the number of reads found in each BAM file is counted. |
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123 Alternatively, an interval file with pre-defined genomic regions can be provided. |
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124 |
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125 In principle, this tool does the same as ``multiBigwigSummary``, but for BAM files. |
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126 |
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127 A typical follow-up application is to check and visualize the similarity and variability between replicates or published data sets (see: ``plotPCA`` and ``plotCorrelation``). |
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128 |
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129 Output |
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130 -------- |
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131 |
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132 The default output is a **compressed file** that can only be used with ``plotPCA`` or ``plotCorrelation``. |
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133 |
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134 To analyze the coverage scores yourself, you can get the **uncompressed score matrix** where every row corresponds to a genomic region (or bin) and each column corresponds to a sample (BAM file). (To obtain this output file, select "Save raw counts (coverages) to file" ) |
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135 |
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136 .. image:: $PATH_TO_IMAGES/multiBamSummary_output.png |
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137 :width: 600 |
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138 :height: 443 |
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139 |
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140 ----- |
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141 |
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142 @REFERENCES@ |
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143 ]]> |
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144 </help> |
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145 <expand macro="citations" /> |
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146 </tool> |