Mercurial > repos > bgruening > deeptools_compute_gc_bias
changeset 8:3d2d0cf4fd17 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
| author | bgruening |
|---|---|
| date | Wed, 23 Dec 2015 14:39:27 -0500 |
| parents | f1b7a3555d34 |
| children | 6524650fadf7 |
| files | computeGCBias.xml deepTools_macros.xml |
| diffstat | 2 files changed, 33 insertions(+), 34 deletions(-) [+] |
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--- a/computeGCBias.xml Wed Dec 23 07:30:00 2015 -0500 +++ b/computeGCBias.xml Wed Dec 23 14:39:27 2015 -0500 @@ -64,17 +64,17 @@ <when value="no" /> <when value="yes"> <param name="sampleSize" type="integer" value="50000000" min="1" - label="Number of sampling points to be considered" help="(--sampleSize)" /> + label="Number of sampling points to consider" help="(--sampleSize)" /> <param name="regionSize" type="integer" value="300" min="1" label="Region size" help ="To plot the reads per GC over a region, the size of the region is - required (see below for more details of the mthod). By default, the bin size - is set to 300 bp, which is close to the standard fragment size many sequencing + required (see below for more details about the method). By default, the bin size + is set to 300 bases, which is close to the standard fragment size of many sequencing applications. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read. (--regionSize)"/> <param name="filterOut" type="data" format="bed" optional="true" label="BED file containing genomic regions to be excluded from the estimation of the correction" - help="Such regions usually contain repetitive regions and peaks that if included will + help="Such regions usually contain repetitive regions and peaks that, if included, would bias the correction. It is recommended to filter out known repetitive regions if multi-reads (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" /> @@ -130,19 +130,19 @@ <![CDATA[ **What it does** -This tool computes the GC bias using the method proposed by Benjamini and Speed (2012) Nucleic Acids Res. (see below for more explanations) +This tool computes the GC bias using the method proposed in Benjamini and Speed (2012) Nucleic Acids Res. (see below for further details). The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias. -There are two plots produced by the tool: a boxplot showing the absolute read numbers per genomic-GC bin and an x-y plot -depicting the ratio of observed/expected reads per genomic GC content bin. +There are two plots produced by the tool: a boxplot showing the absolute read numbers per GC-content bin and an x-y plot +depicting the ratio of observed/expected reads per GC-content bin. ----- **Summary of the method used** -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 -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...). -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 -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). +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 +reference genome contains with each percentage of GC content, i.e. how many regions in the genome have 50% GC (or 10% GC or 90% GC or...). +We then sample a large number of equally sized genomic 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 +sequencing bias and is purely dependent on the underlying genome (i.e. it will most likely vary between mouse and fruit fly due to their genome's different GC contents). 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. 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 usually shows a significant bias towards reads with high GC content (>50%) @@ -157,8 +157,8 @@ - Diagnostic plot - - box plot of absolute read numbers per genomic GC bin - - x-y plot of observed/expected read ratios per genomic GC content bin + - box plot of absolute read numbers per GC-content bin + - x-y plot of observed/expected read ratios per GC-content bin - Data matrix
--- a/deepTools_macros.xml Wed Dec 23 07:30:00 2015 -0500 +++ b/deepTools_macros.xml Wed Dec 23 14:39:27 2015 -0500 @@ -55,7 +55,7 @@ <xml name="includeZeros"> <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" label="Include zeros" - help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." /> + help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." /> </xml> <xml name="zMin_zMax"> @@ -68,7 +68,7 @@ <xml name="region_limit_operation"> <param argument="--region" type="text" value="" label="Region of the genome to limit the operation to" - help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> + help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> @@ -86,8 +86,8 @@ <xml name="smoothLength"> <param argument="--smoothLength" type="integer" value="" optional="True" min="1" - label="Smooth values using the following length (in bp)" - help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> + label="Smooth values using the following length (in bases)" + help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> </xml> @@ -107,11 +107,10 @@ </param> <when value="kmeans"> <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" - help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. - Only works for data that is not grouped, otherwise only the first group will be clustered. + help="When this option is set, the matrix is split into clusters using the k-means algorithm. + This only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and - run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) - if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/> + run the clustering using other software."/> </when> <when value="none" /> </conditional> @@ -157,11 +156,11 @@ <conditional name="doExtendCustom"> <param name="doExtend" type="select" label="Extend reads to the given average fragment size." help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here. - By default *each* read mate is extended. - This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. - Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value. - Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not - recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> + By default *each* read mate is extended. + This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. + Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. + Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not + recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> <option value="custom">A custom length, which will be applied to ALL reads.</option> @@ -189,14 +188,14 @@ help="By default, bamCorrelate considers consecutive bins of the specified 'Bin size'. However, to reduce the computation time, a larger distance between bins can - by given. Larger distances result in less bins being + be given. Larger distances result in fewer bins being considered."/> </xml> <xml name="centerReads"> <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" label="Center regions with respect to the fragment length" - help="For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. "/> + help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/> </xml> <xml name="ignoreDuplicates"> @@ -229,19 +228,19 @@ <xml name="minMappingQuality"> <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1" label="Minimum mapping quality" - help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> + help= "If set, only reads with a mapping quality score higher than this value are considered."/> </xml> <xml name="skipZeros"> <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label ="Skip zeros" - help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." /> + help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." /> </xml> <xml name="fragmentLength"> <param argument="--fragmentLength" type="integer" value="300" min="1" label="Fragment length used for the sequencing" - help ="If paired-end reads are used, the fragment length is computed from the BAM file."/> + help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/> </xml> <xml name="scaleFactor"> @@ -302,7 +301,7 @@ <xml name="multiple_input_bigwigs"> <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" label="Bigwig file" - help="The Bigwig file must be sorted."/> + help="A Bigwig file."/> </xml> <xml name="plotTitle"> @@ -394,8 +393,8 @@ should be skipped. The default is to treat those regions as having a value of zero. The decision to skip non-covered regions depends on the interpretation - of the data. Non-covered regions may represent for - example repetitive regions that want to be skipped. + of the data. Non-covered regions may represent, for + example, repetitive regions that should be ignored. (default: False)" /> </xml>