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comparison bamCorrelate.xml @ 24:d7c9fd76e41e draft

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author bgruening
date Tue, 04 Feb 2014 09:12:07 -0500
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141 This tool is useful to assess the overall similarity of different BAM files. A typical application 141 This tool is useful to assess the overall similarity of different BAM files. A typical application
142 is to check the correlation between replicates or published data sets. 142 is to check the correlation between replicates or published data sets.
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144 The tool splits the genomes into bins of given length. For each bin, the number of reads 144 The tool splits the genomes into bins of given length. For each bin, the number of reads
145 found in each BAM file is counted and a correlation is computed for all 145 found in each BAM file is counted and a correlation (either Pearson or Spearman) is computed for all
146 pairs of BAM files. 146 pairs of BAM files. Finally, a heatmap is drawn based on the similarity of the samples.
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149 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png 149 .. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
150 :alt: Heatmap of RNA Polymerase II ChIP-seq 150 :alt: Heatmap of RNA Polymerase II ChIP-seq
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153 You can find more details in the `bamCorrelate wiki`_. 153 You can find more details on the bamCorrelate wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamCorrelate
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155 .. _bamCorrelate wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
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158 **Output files**: 156 **Output files**:
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160 - diagnostic plot produced by bamCorrelate is a clustered heatmap displaying the values for each pair-wise correlation, see below for an example 158 - **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example
161 - data matrix (optional) in case you want to plot the correlation values using a different program, e.g. R, this matrix can be used 159 - data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used
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166 @REFERENCES@ 164 @REFERENCES@