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comparison bamCompare.xml @ 37:2f7edf06a5da draft

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Uploaded
author bgruening
date Sat, 01 Feb 2014 06:04:58 -0500
parents 934b9fccabd4
children 20f8dafb554f
comparison
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36:ea2f64efe70d 37:2f7edf06a5da
35 35
36 #if $comparison.type=='subtract': 36 #if $comparison.type=='subtract':
37 #if $comparison.normalization.type=='rpkm': 37 #if $comparison.normalization.type=='rpkm':
38 --normalizeUsingRPKM 38 --normalizeUsingRPKM
39 #elif $comparison.normalization.type=='1x': 39 #elif $comparison.normalization.type=='1x':
40 --normalizeTo1x $comparison.normalization.normalizeTo1x 40
41 #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
42 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
43 #else:
44 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
45 #end if
46
41 #end if 47 #end if
42 #end if 48 #end if
43 49
44 #if $advancedOpt.showAdvancedOpt == "yes": 50 #if $advancedOpt.showAdvancedOpt == "yes":
45 #if $advancedOpt.smoothLength: 51 #if $advancedOpt.smoothLength:
121 <option value="no">Do not normalize or scale</option> 127 <option value="no">Do not normalize or scale</option>
122 </param> 128 </param>
123 <when value="rpkm" /> 129 <when value="rpkm" />
124 <when value="no" /> 130 <when value="no" />
125 <when value="1x"> 131 <when value="1x">
126 <param name="normalizeTo1x" type="integer" value="2150570000" 132 <expand macro="effectiveGenomeSize" />
127 label="Report normalized coverage to 1x sequenceing depth"
128 help ="Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
129 </when> 133 </when>
130 </conditional> 134 </conditional>
131 </when> 135 </when>
132 </conditional> 136 </conditional>
133 137
201 205
202 206
203 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png 207 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
204 208
205 209
210 You can find more details in the `bamCompare wiki`_.
211
212 .. _bamCompare wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
213
214
206 **Output files**: 215 **Output files**:
207 216
208 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files. 217 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.
209 218
210 ----- 219 -----
211 220
212 .. class:: infomark 221 @REFERENCES@
213 222
214 </help> 223 </help>
215 </tool> 224 </tool>