Mercurial > repos > mvdbeek > damidseq_core

annotate damidseq_core.xml @ 7:02f09108bcff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit af291f882257a8540e984c177f2a92ec1cfa6fde
author mvdbeek
date Fri, 20 Apr 2018 06:25:32 -0400
parents 9b13b8bda9d8
children 621837e9bfed
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1 <tool id="damidseq_core" name="damidseq" version="0.1.4">
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2 <description>align, extend and normalize a DamID-seq experiment</description>
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3 <requirements>
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4 <requirement type="package" version="1.4">damidseq_pipeline</requirement>
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5 </requirements>
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6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 #set dam_file = 'A001.fastq.gz' if str($dam.ext).endswith('.gz') else 'A001.fastq'
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9 #set dam_fusion_file = 'A002.fastq.gz' if str($dam_fusion.ext).endswith('.gz') else 'A002.fastq'
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10 ln -f -s '$dam' $dam_file &&
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11 ln -f -s '$dam_fusion' $dam_fusion_file &&
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12 ln -f -s '$index' index.txt &&
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13 HOME="\$PWD" damidseq_pipeline
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14 --bins=$bins
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15 --bowtie=1
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16 --bowtie2_genome_dir='$reference_index.fields.path'
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17 --extend_reads=$extend_reads
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18 --extension_method='$extension_method'
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19 $full_data_files
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20 --gatc_frag_file='$gatc_frag_file'
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21 --len=$len
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22 --max_norm_value='$max_norm_value'
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23 $method_subtract
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24 --min_norm_value='$min_norm_value'
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25 --norm_method=$norm_method
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26 --norm_steps=$norm_steps
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27 --output_format=$output_format
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28 --q=$q
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29 --qscore1max=$qscore1max
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30 --qscore1min=$qscore1min
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31 --qscore2max=$qscore2max
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32 --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' &&
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33 mv Fusion-vs-Dam.gatc.* gatc.output
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34 #if str($full_data_files):
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35 && mv Fusion-vs-Dam.* full.output
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36 #end if
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37 ]]></command>
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38 <configfiles>
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39 <configfile name="index">A1 Dam
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40 A2 Fusion</configfile>
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41 </configfiles>
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42 <inputs>
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43 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
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44 <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
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45 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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46 <options from_data_table="bowtie2_indexes">
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47 <filter type="sort_by" column="2"/>
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48 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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49 </options>
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50 </param>
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51 <param argument="--gatc_frag_file" type="data" format="gff" label="GFF file with all GATC locations"/>
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52 <param name="output_format" type="select" label="Select the output format for the peaks">
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53 <option value="bedgraph">Bed</option>
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54 <option value="gff">GFF</option>
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55 </param>
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56 <param argument="--extend_reads" type="boolean" truevalue="1" falsevalue="0" checked="True" label="Perform read extension?"/>
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57 <param argument="--extension_method" type="select" label="Select the read extension method" help="Select Full to extend all reads or GATC to extend reads to --len or to the next GATC site, whichever is shorter. Using this option increases peak resolution (default).">
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58 <option value="gatc">To nearest GATC site</option>
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59 <option value="full">Full</option>
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60 </param>
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61 <param argument="--full_data_files" type="boolean" truevalue="--full_data_files" falsevalue="" label="Output full binned ratio files (not only GATC array)"/>
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62 <param argument="--len" type="integer" min="50" value="300" label="Length to extend reads to"/>
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63 <param argument="--bins" type="integer" min="10" value="75" label="Width of bins to use for mapping reads"/>
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64 <param argument="--min_norm_value" type="float" value="-5.0" label="Minimum log2 value to limit normalisation search at"/>
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65 <param argument="--max_norm_value" type="float" value="5.0" label="Maximum log2 value to limit normalisation search at"/>
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66 <param argument="--method_subtract" type="boolean" truevalue="--method_subtract" falsevalue="" label="Subtract Dam control values from Dam-fusion values instead of using the log2 ratio?"/>
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67 <param argument="--norm_method" type="select" label="Select normalization method">
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68 <option value="kde">kernel density estimation of log2 GATC fragment ratio (recommended)</option>
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69 <option value="rpm">readcounts per million reads (not recommended for most use cases)</option>
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70 </param>
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71 <param argument="--norm_steps" type="integer" min="1" value="300" label="Number of points in normalisation routine"/>
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72 <param argument="--q" type="integer" value="30" min="0" label="Cutoff average Q score for aligned reads"/>
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73 <param argument="--qscore1min" type="float" min="0.0" value="0.4" max="1.0" label="min decile for normalising from Dam array"/>
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74 <param argument="--qscore1max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from Dam array"/>
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75 <param argument="--qscore2max" type="float" min="0.0" value="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/>
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76 </inputs>
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77 <outputs>
6
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78 <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}">
0
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79 <change_format>
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80 <when input="output_format" value="gff" format="gff" />
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81 </change_format>
1
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82 <actions>
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83 <action type="metadata" name="dbkey">
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84 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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85 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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86 <filter type="param_value" ref="reference_index" column="0"/>
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87 </option>
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88 </action>
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89 </actions>
0
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90 </data>
6
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91 <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}">
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92 <filter>full_data_files</filter>
6
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93 <change_format>
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94 <when input="output_format" value="gff" format="gff" />
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95 </change_format>
1
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96 <actions>
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97 <action type="metadata" name="dbkey">
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98 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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99 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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100 <filter type="param_value" ref="reference_index" column="0"/>
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101 </option>
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102 </action>
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103 </actions>
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104 </data>
6
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105 <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="Dam-only alignment on ${on_string}">
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106 <actions>
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107 <action type="metadata" name="dbkey">
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108 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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109 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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110 <filter type="param_value" ref="reference_index" column="0"/>
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111 </option>
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112 </action>
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113 </actions>
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114 </data>
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115 <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="Dam-fusion alignment on ${on_string}">
1
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116 <actions>
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117 <action type="metadata" name="dbkey">
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118 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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119 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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120 <filter type="param_value" ref="reference_index" column="0"/>
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121 </option>
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122 </action>
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123 </actions>
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124 </data>
0
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125 </outputs>
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126 <tests>
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127 <test>
5
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128 <param name="dam" value="A001.fastq.gz"/>
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129 <param name="dam_fusion" value="A002.fastq.gz"/>
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130 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
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131 <param name="reference_index" value="dm6"/>
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132 <param name="norm_method" value="rpm"/>
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133 <output name="output_ratio" file="output_ratio.bed"/>
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134 <output name="control_output" file="control.bam"/>
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135 <output name="fusion_output" file="fusion.bam"/>
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136 </test>
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137 <test>
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138 <param name="dam" value="A001.fastq"/>
0
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139 <param name="dam_fusion" value="A002.fastq"/>
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140 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
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141 <param name="reference_index" value="dm6"/>
0
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142 <param name="norm_method" value="rpm"/>
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143 <param name="full_data_files" value="true"/>
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144 <output name="output_ratio" file="output_ratio.bed"/>
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145 <output name="output_ratio_full" file="output_ratio_full.bed"/>
0
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146 <output name="control_output" file="control.bam"/>
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147 <output name="fusion_output" file="fusion.bam"/>
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151
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152 Processing DamID-seq data involves extending single-end reads, aligning
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153 the reads to the genome and determining the coverage, similar to
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154 processing regular ChIP-seq datasets. However, as DamID data is
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155 represented as a log2 ratio of (Dam-fusion/Dam), normalisation of the
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156 sample and Dam-only control is necessary and adding pseudocounts to
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157 mitigate the effect of background counts is highly recommended.
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158
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159 damidseq_pipeline is a single script that automatically handles
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160 sequence alignment, read extension, binned counts, normalisation,
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161 pseudocount addition and final ratio file generation. The script uses
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162 FASTQ or BAM files as input, and outputs the final log2 ratio files in
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163 bedGraph (or optionally GFF) format.
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164
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165 The output ratio files can easily be converted to TDF for viewing in IGV using
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166 igvtools. The files can be processed for peak calling using find_peaks or, if
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167 using RNA pol II DamID, transcribed genes can be determined using
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168 polii.gene.call.
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169
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170 ]]></help>
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171 <citations>
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172 <citation type="doi">10.1093/bioinformatics/btv386</citation>
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173 </citations>
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174 </tool>