Mercurial > repos > bgruening > diffbind

comparison diffbind.xml @ 12:fa56d93f7980 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
author iuc
date Thu, 19 Apr 2018 17:15:53 -0400
parents 4c7ab9995f9e
children 1de83981d43c
comparison
equal deleted inserted replaced
11:4c7ab9995f9e 12:fa56d93f7980
1 <tool id="diffbind" name="DiffBind" version="2.6.6.1"> 1 <tool id="diffbind" name="DiffBind" version="2.6.6.2">
2 <description> differential binding analysis of ChIP-Seq peak data</description> 2 <description> differential binding analysis of ChIP-Seq peak data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement> 4 <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement>
5 <requirement type="package" version="1.20.0">r-getopt</requirement> 5 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="0.2.15">r-rjson</requirement> 6 <requirement type="package" version="0.2.15">r-rjson</requirement>
15 level="fatal" 15 level="fatal"
16 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> 16 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
17 <regex match="Error in" 17 <regex match="Error in"
18 source="both" 18 source="both"
19 level="fatal" 19 level="fatal"
20 description="An undefined error occured, please check your intput carefully and contact your administrator." /> 20 description="An undefined error occured, please check your input carefully and contact your administrator." />
21 </stdio> 21 </stdio>
22 <version_command><![CDATA[ 22 <version_command><![CDATA[
23 echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 23 echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
24 ]]></version_command> 24 ]]></version_command>
25 <command><![CDATA[ 25 <command><![CDATA[
63 #end if 63 #end if
64 64
65 #end for 65 #end for
66 66
67 $temp_factor.reverse() 67 $temp_factor.reverse()
68 $temp_factor_names.append([str($factorName), $temp_factor]) 68 $temp_factor_names.append(["Condition", $temp_factor])
69 69
70 70
71 Rscript '$__tool_directory__/diffbind.R' 71 Rscript '$__tool_directory__/diffbind.R'
72 72
73 -i '#echo json.dumps(temp_factor_names)#' 73 -i '#echo json.dumps(temp_factor_names)#'
102 && cp '$__tool_directory__/diffbind.R' '$rscript' 102 && cp '$__tool_directory__/diffbind.R' '$rscript'
103 #end if 103 #end if
104 ]]> 104 ]]>
105 </command> 105 </command>
106 <inputs> 106 <inputs>
107 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Condition). One factor must be entered and there must be two or more groups. NOTE: Please only use letters, numbers or underscores."> 107 <repeat name="rep_group" title="Group" min="2" max="2" default="2">
108 <sanitizer>
109 <valid initial="string.letters,string.digits"><add value="_" /></valid>
110 </sanitizer>
111 </param>
112 <repeat name="rep_group" title="Group" min="2" default="2">
113 <param name="groupName" type="text" label="Name" 108 <param name="groupName" type="text" label="Name"
114 help="Name of group that the peak files belong to (e.g. Resistant or Responsive). NOTE: Please only use letters, numbers or underscores (case sensitive)."> 109 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups in total must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">
115 <sanitizer> 110 <sanitizer>
116 <valid initial="string.letters,string.digits"><add value="_" /></valid> 111 <valid initial="string.letters,string.digits"><add value="_" /></valid>
117 </sanitizer> 112 </sanitizer>
113 <validator type="empty_field" />
118 </param> 114 </param>
119 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/> 115 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
120 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM file" help="Specify the Read BAM file used for Peak calling."/> 116 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM file" help="Specify the Read BAM file used in the Peak calling."/>
121 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM file" help="If specifying a control BAM file, all samples are required to specify one."/> 117 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM file" help="If specifying a control BAM file, all samples are required to specify one, see Help section below."/>
122 </repeat> 118 </repeat>
123 119
124 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)"/> 120 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)">
121 <sanitizer>
122 <valid initial="string.digits"/>
123 </sanitizer>
124 </param>
125 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" /> 125 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" />
126 <param name="summits" type="integer" min="0" optional="True" label="Summits" help="Extend peaks Nbp up- and downstream of the summit. For punctate peaks it is advisable to extend (e.g. 250bp), see the DiffBind User Guide"/> 126 <param name="summits" type="integer" min="0" optional="True" label="Summits" help="Extend peaks Nbp up- and downstream of the summit. For punctate peaks it is advisable to extend (e.g. 250bp), see the DiffBind User Guide">
127 <sanitizer>
128 <valid initial="string.digits"/>
129 </sanitizer>
130 </param>
127 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/> 131 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/>
128 132
129 <!-- Output Options --> 133 <!-- Output Options -->
130 <section name="out" expanded="false" title="Output Options"> 134 <section name="out" expanded="false" title="Output Options">
131 <param name="format" type="select" label="Output Format"> 135 <param name="format" type="select" label="Output Format">
140 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/> 144 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/>
141 </section> 145 </section>
142 </inputs> 146 </inputs>
143 147
144 <outputs> 148 <outputs>
145 <data name="outfile" format="bed" label="${tool.name} on ${on_string}: Differentially bound sites"> 149 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}: Differentially bound sites" />
146 <change_format>
147 <when input="format" value="wig" format="wig" />
148 <when input="format" value="gff" format="gff" />
149 </change_format>
150 </data>
151 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots"> 150 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots">
152 <filter>out['pdf']</filter> 151 <filter>out['pdf']</filter>
153 </data> 152 </data>
154 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix"> 153 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix">
155 <filter>out['binding_matrix']</filter> 154 <filter>out['binding_matrix']</filter>
165 </data> 164 </data>
166 </outputs> 165 </outputs>
167 166
168 <tests> 167 <tests>
169 <test expect_num_outputs="6"> 168 <test expect_num_outputs="6">
170 <param name="factorName" value="Condition"/>
171 <repeat name="rep_group"> 169 <repeat name="rep_group">
172 <param name="groupName" value="Resistant"/> 170 <param name="groupName" value="Resistant"/>
173 <param name="peaks" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> 171 <param name="peaks" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
174 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> 172 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
175 </repeat> 173 </repeat>
182 <param name="pdf" value="True" /> 180 <param name="pdf" value="True" />
183 <param name="binding_matrix" value="True" /> 181 <param name="binding_matrix" value="True" />
184 <param name="rdata" value="True" /> 182 <param name="rdata" value="True" />
185 <param name="rscript" value="True"/> 183 <param name="rscript" value="True"/>
186 <param name="analysis_info" value="True"/> 184 <param name="analysis_info" value="True"/>
187 <output name="outfile" value="out_diffbind.bed" /> 185 <output name="outfile" value="out_diffbind.tab" />
188 <output name="plots" value="out_plots.pdf" compare="sim_size" /> 186 <output name="plots" value="out_plots.pdf" compare="sim_size" />
189 <output name="binding_matrix" value="out_binding.matrix" /> 187 <output name="binding_matrix" value="out_binding.matrix" />
190 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/> 188 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/>
191 <output name="rscript" value="out_rscript.txt"/> 189 <output name="rscript" value="out_rscript.txt"/>
192 <output name="analysis_info" value="out_analysis_info.txt" compare="sim_size" > 190 <output name="analysis_info" value="out_analysis_info.txt" compare="sim_size" >
233 231
234 DiffBind works primarily with peaksets, which are sets of genomic intervals representing 232 DiffBind works primarily with peaksets, which are sets of genomic intervals representing
235 candidate protein binding sites. Each interval consists of a chromosome, a start and end 233 candidate protein binding sites. Each interval consists of a chromosome, a start and end
236 position, and usually a score of some type indicating confidence in, or strength of, the peak. 234 position, and usually a score of some type indicating confidence in, or strength of, the peak.
237 Associated with each peakset are metadata relating to the experiment from which the peakset 235 Associated with each peakset are metadata relating to the experiment from which the peakset
238 was derived. Additionally, files containing mapped sequencing reads (generally .bam files) can 236 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to
239 be associated with each peakset (one for the ChIP data, and optionally another representing 237 be associated with each peakset (one for the ChIP data, and optionally another representing
240 a control sample) 238 a control sample)
241 239
242 **Sample Information** 240 **Groups**
243 241
244 You have to specify your sample information in the tool form above, where Factor is the groups you want to compare (e.g Resistant and Responsive). 242 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above.
245 243
246 Example: 244 Example:
247 245
248 ============= ============= 246 ============= =============
249 **SampleID** **Group** 247 **Sample** **Group**
250 ------------- ------------- 248 ------------- -------------
251 BT4741 Resistant 249 BT4741 Resistant
252 BT4742 Resistant 250 BT4742 Resistant
253 MCF71 Responsive 251 MCF71 Responsive
254 MCF72 Responsive 252 MCF72 Responsive
257 255
258 **Peak files** 256 **Peak files**
259 257
260 Result of your Peak calling experiment in bed format, one file for each sample is required. The peak caller, format and score column can be specified in the tool form above. The default settings expect narrowPeak bed format, which has the score in the 8th column (-log10pvalue), and can be output from MACS2. 258 Result of your Peak calling experiment in bed format, one file for each sample is required. The peak caller, format and score column can be specified in the tool form above. The default settings expect narrowPeak bed format, which has the score in the 8th column (-log10pvalue), and can be output from MACS2.
261 259
262 Example (MACS.xls file in bed format): 260 Example:
263 261
264 ======= ======= ======= =============== ============== 262 ======= ======= ======= =============== ==============
265 1 2 3 4 **5 (Score)** 263 1 2 3 4 **5 (Score)**
266 ======= ======= ======= =============== ============== 264 ======= ======= ======= =============== ==============
267 chr18 215562 216063 MACS_peak_16037 56.11 265 chr18 215562 216063 peak_16037 56.11
268 chr18 311530 312105 MACS_peak_16038 222.49 266 chr18 311530 312105 peak_16038 222.49
269 chr18 356656 357315 MACS_peak_16039 92.06 267 chr18 356656 357315 peak_16039 92.06
270 chr18 371110 372092 MACS_peak_16040 123.86 268 chr18 371110 372092 peak_16040 123.86
271 chr18 395116 396464 MACS_peak_16041 1545.39 269 chr18 395116 396464 peak_16041 1545.39
272 chr18 399014 400382 MACS_peak_16042 1835.19 270 chr18 399014 400382 peak_16042 1835.19
273 chr18 499134 500200 MACS_peak_16043 748.32 271 chr18 499134 500200 peak_16043 748.32
274 chr18 503518 504552 MACS_peak_16044 818.30 272 chr18 503518 504552 peak_16044 818.30
275 chr18 531672 532274 MACS_peak_16045 159.30 273 chr18 531672 532274 peak_16045 159.30
276 chr18 568326 569282 MACS_peak_16046 601.11 274 chr18 568326 569282 peak_16046 601.11
277 ======= ======= ======= =============== ============== 275 ======= ======= ======= =============== ==============
278 276
279 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required. 277 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required.
280 * Optional: Control BAM file representing a control dataset. If used, has to be specified for all samples. Note that the DiffBind authors say control reads are best utilized prior to running DiffBind, at the peak calling stage (e.g. with MACS2) and in blacklists, see this `Bioconductor post`_. 278 * Optional: Control BAM file representing a control dataset. If used, has to be specified for all samples. Note that the DiffBind authors say control reads are best utilized prior to running DiffBind, at the peak calling stage (e.g. with MACS2) and in blacklists, see this `Bioconductor post`_.
281 279
283 281
284 **Outputs** 282 **Outputs**
285 283
286 This tool outputs 284 This tool outputs
287 285
288 * differentially bound sites in BED, WIG or GFF format 286 * a table of differentially bound sites
289 287
290 Optionally, under **Output Options** you can choose to output 288 Optionally, under **Output Options** you can choose to output
291 289
292 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots) 290 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots)
293 * a binding affinity matrix 291 * a binding affinity matrix
295 * an RData file of the R objects generated 293 * an RData file of the R objects generated
296 * a text file with information on the analysis (number of Intervals, FriP scores, method used) 294 * a text file with information on the analysis (number of Intervals, FriP scores, method used)
297 295
298 **Differentially Bound Sites** 296 **Differentially Bound Sites**
299 297
300 As output format you can choose BED, GFF, WIG. 298 Example:
301 299
302 Example - BED format: 300 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ========
303 301 seqnames start end width strand Conc Conc_Responsive Conc_Resistant Fold p.value **FDR**
304 ======== ====== ====== ===== ====== ===== =============== ============== ======= ======== ======== 302 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ========
305 seqnames start end width strand Conc Conc_Responsive Conc_Resistant Fold p.value **FDR** 303 chr18 394600 396513 1914 \* 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21
306 ======== ====== ====== ===== ====== ===== =============== ============== ======= ======== ======== 304 chr18 111567 112005 439 \* 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06
307 chr18 394600 396513 1914 * 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21 305 chr18 346464 347342 879 \* 5 5.77 3.24 2.52 6.51e-06 0.00303
308 chr18 111567 112005 439 * 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06 306 chr18 399014 400382 1369 \* 7.62 7 8.05 -1.04 1.04e-05 0.00364
309 chr18 346464 347342 879 * 5 5.77 3.24 2.52 6.51e-06 0.00303 307 chr18 371110 372102 993 \* 4.63 3.07 5.36 -2.3 8.1e-05 0.0226
310 chr18 399014 400382 1369 * 7.62 7 8.05 -1.04 1.04e-05 0.00364 308 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ========
311 chr18 371110 372102 993 * 4.63 3.07 5.36 -2.3 8.1e-05 0.0226 309
312 ======== ====== ====== ===== ====== ===== =============== ============== ======= ======== ======== 310 Columns contain the following data:
313 311
314 Columns contain the following data: 312 * **seqnames**: Chromosome name
315 313 * **start**: Start position of site
316 * **1st**: Chromosome name 314 * **end**: End position of site
317 * **2nd**: Start position of site 315 * **width**: Length of site
318 * **3rd**: End position of site 316 * **strand**: Strand
319 * **4th**: Length of site 317 * **Conc**: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)
320 * **5th**: Strand 318 * **Responsive**: Mean concentration over the first (e.g. Responsive) group
321 * **6th**: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) 319 * **Resistant**: Mean concentration over second (e.g. Resistant) group
322 * **7th**: Mean concentration over the first (e.g. Resistant) group 320 * **Fold**: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group.
323 * **8th**: Mean concentration over second (e.g. Responsive) group 321 * **p.value**: P-value confidence measure for identifying these sites as differentially bound
324 * **9th**: Fold shows the difference in mean concentrations between the two groups (e.g. Resistant - Responsive), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group. 322 * **FDR**: a multiple testing corrected FDR p-value
325 * **10th**: P-value confidence measure for identifying these sites as differentially bound
326 * **11th**: a multiple testing corrected FDR p-value
327 323
328 324
329 **Binding Affinity Matrix** 325 **Binding Affinity Matrix**
330 326
331 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent 327 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent
332 differential analysis. 328 differential analysis.
333 329
334 Example: 330 Example:
335 331
336 ===== ====== ====== ================ ================ ================ ================ 332 ===== ====== ====== ========= ========= ========== ==========
337 CHR START END MCF7_ER_1.bed MCF7_ER_2.bed BT474_ER_1.bed BT474_ER_2.bed 333 CHR START END MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2
338 ===== ====== ====== ================ ================ ================ ================ 334 ===== ====== ====== ========= ========= ========== ==========
339 chr18 111567 112005 137.615208000375 59.878372946728 29.4139375878664 19.9594576489093 335 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945
340 chr18 189223 189652 19.9594576489093 12.6059732519427 11.5554754809475 23.110950961895 336 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095
341 chr18 215232 216063 11.5554754809475 15.7574665649284 31.5149331298568 72.4843461986707 337 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434
342 chr18 311530 312172 17.8584621069189 11.5554754809475 54.6258840917518 43.0704086108043 338 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040
343 chr18 346464 347342 75.6358395116564 40.9694130688139 21.0099554199046 16.8079643359236 339 chr18 346464 347342 75.63583 40.96941 21.00995 16.80796
344 chr18 356560 357362 11.5554754809475 14.7069687939332 57.7773774047375 53.5753863207566 340 chr18 356560 357362 11.55547 14.70696 57.77737 53.57538
345 chr18 371110 372102 8.40398216796182 9.45447993895705 81.9388261376278 82.989323908623 341 chr18 371110 372102 8.403982 9.454479 81.93882 82.98932
346 chr18 394600 396513 56.7268796337423 43.0704086108043 510.541916703681 438.05757050501 342 chr18 394600 396513 56.72687 43.07040 510.5419 438.0575
347 chr18 399014 400382 156.524167878289 117.655750351465 558.864814169461 496.885445680743 343 chr18 399014 400382 156.5241 117.6557 558.8648 496.8854
348 chr18 498906 500200 767.913870597511 278.381909313735 196.443083176108 181.736114382174 344 chr18 498906 500200 767.9138 278.3819 196.4430 181.7361
349 ===== ====== ====== ================ ================ ================ ================ 345 ===== ====== ====== ========= ========= ========== ==========
350 346
351 ----- 347 -----
352 348
353 **More Information** 349 **More Information**
354 350
402 398
403 The core functionality of DiffBind is the 399 The core functionality of DiffBind is the
404 differential binding affinity analysis, which enables binding sites to be identified that 400 differential binding affinity analysis, which enables binding sites to be identified that
405 are statistically significantly differentially bound between sample groups. To accomplish 401 are statistically significantly differentially bound between sample groups. To accomplish
406 this, first a contrast (or contrasts) is established, dividing the samples into groups to 402 this, first a contrast (or contrasts) is established, dividing the samples into groups to
407 be compared. Next the core analysis routines are executed, by default using DESeq2 . 403 be compared. Next the core analysis routines are executed, by default using DESeq2.
408 This will assign a p-value and FDR to each candidate binding site indicating confidence 404 This will assign a p-value and FDR to each candidate binding site indicating confidence
409 that they are differentially bound. 405 that they are differentially bound.
410 406
411 **Plotting and reporting**: 407 **Plotting and reporting**:
412 408