deeptools: computeGCBias.xml annotate

annotate computeGCBias.xml @ 30:5231f398d784 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty

author	bgruening
date	Tue, 20 Oct 2015 14:43:12 -0400
parents	3a2aab18a217
children

rev	line source
28 f7712a057440 new bugfix release bgruening parents: 27 diff changeset	1 <tool id="deeptools_computeGCBias" name="computeGCBias" version="@WRAPPER_VERSION@.0">
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	2 <description>to see whether your samples should be normalized for GC bias</description>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	3 <macros>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	4 <token name="@BINARY@">computeGCBias</token>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	5 <import>deepTools_macros.xml</import>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	6 </macros>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	7 <expand macro="requirements" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	8 <command>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	9 <![CDATA[
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	10 ln -s $bamInput local_bamInput.bam;
2ad3b027dfcd Uploaded bgruening parents: diff changeset	11 ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
2ad3b027dfcd Uploaded bgruening parents: diff changeset	12
2ad3b027dfcd Uploaded bgruening parents: diff changeset	13 computeGCBias
2ad3b027dfcd Uploaded bgruening parents: diff changeset	14 @THREADS@
2ad3b027dfcd Uploaded bgruening parents: diff changeset	15
2ad3b027dfcd Uploaded bgruening parents: diff changeset	16 --bamfile 'local_bamInput.bam'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	17 --GCbiasFrequenciesFile $outFileName
2ad3b027dfcd Uploaded bgruening parents: diff changeset	18 --fragmentLength $fragmentLength
2ad3b027dfcd Uploaded bgruening parents: diff changeset	19
2ad3b027dfcd Uploaded bgruening parents: diff changeset	20 @reference_genome_source@
2ad3b027dfcd Uploaded bgruening parents: diff changeset	21
2ad3b027dfcd Uploaded bgruening parents: diff changeset	22 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
2ad3b027dfcd Uploaded bgruening parents: diff changeset	23 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
2ad3b027dfcd Uploaded bgruening parents: diff changeset	24 #else:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	25 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
2ad3b027dfcd Uploaded bgruening parents: diff changeset	26 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	27
2ad3b027dfcd Uploaded bgruening parents: diff changeset	28 #if str($region).strip() != '':
2ad3b027dfcd Uploaded bgruening parents: diff changeset	29 --region '$region'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	30 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	31
2ad3b027dfcd Uploaded bgruening parents: diff changeset	32 #if $advancedOpt.showAdvancedOpt == "yes":
2ad3b027dfcd Uploaded bgruening parents: diff changeset	33 --sampleSize '$advancedOpt.sampleSize'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	34 --regionSize '$advancedOpt.regionSize'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	35
2ad3b027dfcd Uploaded bgruening parents: diff changeset	36 #if $advancedOpt.filterOut:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	37 --filterOut $advancedOpt.filterOut
2ad3b027dfcd Uploaded bgruening parents: diff changeset	38 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	39
2ad3b027dfcd Uploaded bgruening parents: diff changeset	40 #if $advancedOpt.extraSampling:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	41 --extraSampling $advancedOpt.extraSampling
2ad3b027dfcd Uploaded bgruening parents: diff changeset	42 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	43 #end if
2ad3b027dfcd Uploaded bgruening parents: diff changeset	44
2ad3b027dfcd Uploaded bgruening parents: diff changeset	45 #if str($image_format) != 'none':
2ad3b027dfcd Uploaded bgruening parents: diff changeset	46 --biasPlot $outImageName
2ad3b027dfcd Uploaded bgruening parents: diff changeset	47 --plotFileFormat $image_format
2ad3b027dfcd Uploaded bgruening parents: diff changeset	48 #end if
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	49 ]]>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	50 </command>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	51 <inputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	52 <param name="bamInput" format="bam" type="data" label="BAM file"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	53 help="The BAM file must be sorted."/>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	54
2ad3b027dfcd Uploaded bgruening parents: diff changeset	55 <expand macro="reference_genome_source" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	56 <expand macro="effectiveGenomeSize" />
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	57 <expand macro="fragmentLength" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	58 <expand macro="region_limit_operation" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	59
2ad3b027dfcd Uploaded bgruening parents: diff changeset	60 <conditional name="advancedOpt">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	61 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
2ad3b027dfcd Uploaded bgruening parents: diff changeset	62 <option value="no" selected="true">no</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	63 <option value="yes">yes</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	64 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	65 <when value="no" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	66 <when value="yes">
2ad3b027dfcd Uploaded bgruening parents: diff changeset	67 <param name="sampleSize" type="integer" value="50000000" min="1"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	68 label="Number of sampling points to be considered" help="(--sampleSize)" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	69 <param name="regionSize" type="integer" value="300" min="1"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	70 label="Region size"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	71 help ="To plot the reads per GC over a region, the size of the region is
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	72 required (see below for more details of the mthod). By default, the bin size
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	73 is set to 300 bp, which is close to the standard fragment size many sequencing
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	74 applications. However, if the depth of sequencing is low, a larger bin size will
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	75 be required, otherwise many bins will not overlap with any read. (--regionSize)"/>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	76 <param name="filterOut" type="data" format="bed" optional="true"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	77 label="BED file containing genomic regions to be excluded from the estimation of the correction"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	78 help="Such regions usually contain repetitive regions and peaks that if included will
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	79 bias the correction. It is recommended to filter out known repetitive regions if multi-reads
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	80 (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data,
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	81 it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	82 <param name="extraSampling" type="data" format="bed" optional="true"
2ad3b027dfcd Uploaded bgruening parents: diff changeset	83 label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	84 help="(--extraSampling)" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	85 </when>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	86 </conditional>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	87 <param name="image_format" type="select"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	88 label="GC bias plot"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	89 help="If given, a diagnostic image summarizing the GC bias found on the sample will be created. (--plotFileFormat)">
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	90 <option value="none">No image</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	91 <option value="png" selected="true">Image in png format</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	92 <option value="pdf">Image in pdf format</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	93 <option value="svg">Image in svg format</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	94 <option value="eps">Image in eps format</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	95 <option value="emf">Image in emf format</option>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	96 </param>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	97 </inputs>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	98 <outputs>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	99 <data name="outFileName" format="tabular" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	100 <data name="outImageName" format="png" label="${tool.name} GC-bias Plot">
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	101 <filter>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	102 ((
2ad3b027dfcd Uploaded bgruening parents: diff changeset	103 image_format != 'none'
2ad3b027dfcd Uploaded bgruening parents: diff changeset	104 ))
2ad3b027dfcd Uploaded bgruening parents: diff changeset	105 </filter>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	106 <change_format>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	107 <when input="image_format" value="pdf" format="pdf" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	108 <when input="image_format" value="svg" format="svg" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	109 <when input="image_format" value="eps" format="eps" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	110 <when input="image_format" value="emf" format="emf" />
2ad3b027dfcd Uploaded bgruening parents: diff changeset	111 </change_format>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	112 </data>
2ad3b027dfcd Uploaded bgruening parents: diff changeset	113 </outputs>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	114 <tests>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	115 <test>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	116 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	117 <param name="image_format" value="png" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	118 <param name="showAdvancedOpt" value="yes" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	119 <param name="regionSize" value="1" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	120 <param name="fragmentLength" value="100" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	121 <param name="ref_source" value="history" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	122 <param name="input1" value="sequence.2bit" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	123 <param name="sampleSize" value="10" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	124 <param name="effectiveGenomeSize_opt" value="specific" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	125 <param name="effectiveGenomeSize" value="23011544" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	126 <param name="region" value="chr2L" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	127 <param name="image_format" value="none" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	128 <output name="outFileName" file="computeGCBias_result1.tabular" ftype="tabular" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	129 </test>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	130 </tests>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	131 <help>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	132 <![CDATA[
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	133 What it does
2ad3b027dfcd Uploaded bgruening parents: diff changeset	134
2ad3b027dfcd Uploaded bgruening parents: diff changeset	135 This tool computes the GC bias using the method proposed by Benjamini and Speed (2012) Nucleic Acids Res. (see below for more explanations)
2ad3b027dfcd Uploaded bgruening parents: diff changeset	136 The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias.
2ad3b027dfcd Uploaded bgruening parents: diff changeset	137 There are two plots produced by the tool: a boxplot showing the absolute read numbers per genomic-GC bin and an x-y plot
2ad3b027dfcd Uploaded bgruening parents: diff changeset	138 depicting the ratio of observed/expected reads per genomic GC content bin.
2ad3b027dfcd Uploaded bgruening parents: diff changeset	139
2ad3b027dfcd Uploaded bgruening parents: diff changeset	140 -----
2ad3b027dfcd Uploaded bgruening parents: diff changeset	141
2ad3b027dfcd Uploaded bgruening parents: diff changeset	142 Summary of the method used
2ad3b027dfcd Uploaded bgruening parents: diff changeset	143
2ad3b027dfcd Uploaded bgruening parents: diff changeset	144 In order to estimate how many reads with what kind of GC content one should have sequenced, we first need to determine how many regions the specific
2ad3b027dfcd Uploaded bgruening parents: diff changeset	145 reference genome contains for each amount of GC content, i.e. how many regions in the genome have 50% GC (or 10% GC or 90% GC or...).
2ad3b027dfcd Uploaded bgruening parents: diff changeset	146 We then sample a large number of equally sized genome bins and count how many times we see a bin with 50% GC (or 10% GC or 90% or...). These EXPECTED values are independent of any
2ad3b027dfcd Uploaded bgruening parents: diff changeset	147 sequencing as it only depends on the respective reference genome (i.e. it will most likely vary between mouse and fruit fly due to their genome's different GC contents).
2ad3b027dfcd Uploaded bgruening parents: diff changeset	148 The OBSERVED values are based on the reads from the sequenced sample. Instead of noting how many genomic regions there are per GC content, we now count the reads per GC content.
2ad3b027dfcd Uploaded bgruening parents: diff changeset	149 In an ideal sample without GC bias, the ratio of OBSERVED/EXPECTED values should be close to 1 regardless of the GC content. Due to PCR (over)amplifications, the majority of ChIP samples
2ad3b027dfcd Uploaded bgruening parents: diff changeset	150 usually shows a significant bias towards reads with high GC content (>50%)
2ad3b027dfcd Uploaded bgruening parents: diff changeset	151
2ad3b027dfcd Uploaded bgruening parents: diff changeset	152 .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png
2ad3b027dfcd Uploaded bgruening parents: diff changeset	153
2ad3b027dfcd Uploaded bgruening parents: diff changeset	154
2ad3b027dfcd Uploaded bgruening parents: diff changeset	155 You can find more details on the computeGCBias wiki page: computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias
2ad3b027dfcd Uploaded bgruening parents: diff changeset	156
2ad3b027dfcd Uploaded bgruening parents: diff changeset	157
2ad3b027dfcd Uploaded bgruening parents: diff changeset	158 Output files:
2ad3b027dfcd Uploaded bgruening parents: diff changeset	159
2ad3b027dfcd Uploaded bgruening parents: diff changeset	160 - Diagnostic plot
2ad3b027dfcd Uploaded bgruening parents: diff changeset	161
2ad3b027dfcd Uploaded bgruening parents: diff changeset	162 - box plot of absolute read numbers per genomic GC bin
2ad3b027dfcd Uploaded bgruening parents: diff changeset	163 - x-y plot of observed/expected read ratios per genomic GC content bin
2ad3b027dfcd Uploaded bgruening parents: diff changeset	164
2ad3b027dfcd Uploaded bgruening parents: diff changeset	165 - Data matrix
2ad3b027dfcd Uploaded bgruening parents: diff changeset	166
2ad3b027dfcd Uploaded bgruening parents: diff changeset	167 - to be used for GC correction with correctGCbias
2ad3b027dfcd Uploaded bgruening parents: diff changeset	168
2ad3b027dfcd Uploaded bgruening parents: diff changeset	169
2ad3b027dfcd Uploaded bgruening parents: diff changeset	170 -----
2ad3b027dfcd Uploaded bgruening parents: diff changeset	171
2ad3b027dfcd Uploaded bgruening parents: diff changeset	172 @REFERENCES@
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	173 ]]>
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	174 </help>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	175 <expand macro="citations" />
26 2ad3b027dfcd Uploaded bgruening parents: diff changeset	176 </tool>

Mercurial > repos > bgruening > deeptools

annotate computeGCBias.xml @ 30:5231f398d784 draft