comparison bamCorrelate.xml @ 24:d7c9fd76e41e draft

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This tool is useful to assess the overall similarity of different BAM files. A typical application
is to check the correlation between replicates or published data sets.

The tool splits the genomes into bins of given length. For each bin, the number of reads
found in each BAM file is counted and a correlation is computed for all
pairs of BAM files.


.. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
   :alt: Heatmap of RNA Polymerase II ChIP-seq


You can find more details in the `bamCorrelate wiki`_.

.. _bamCorrelate wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare


**Output files**:

- diagnostic plot produced by bamCorrelate is a clustered heatmap displaying the values for each pair-wise correlation, see below for an example
- data matrix (optional) in case you want to plot the correlation values using a different program, e.g. R, this matrix can be used


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@REFERENCES@

24:d7c9fd76e41e

This tool is useful to assess the overall similarity of different BAM files. A typical application
is to check the correlation between replicates or published data sets.

The tool splits the genomes into bins of given length. For each bin, the number of reads
found in each BAM file is counted and a correlation (either Pearson or Spearman) is computed for all
pairs of BAM files. Finally, a heatmap is drawn based on the similarity of the samples.


.. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png
   :alt: Heatmap of RNA Polymerase II ChIP-seq


You can find more details on the bamCorrelate wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamCorrelate


**Output files**:

- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example
- 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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@REFERENCES@