comparison bamFingerprint.xml @ 43:c5787c91cab8 draft

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42:ef1232cedacb

<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.3">
    <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">bamFingerprint</token>

          #end if
      #else
        --plotFileFormat 'png'
      #end if

      #if str(region).strip() != '':
          --region 'region'
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
        --binSize '$advancedOpt.binSize'
        --numberOfSamples '$advancedOpt.numberOfSamples'

    </outputs>
    <help>

**What it does**

This tool is based on a method developed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3).
The resulting plot can be used to assess the strength of a ChIP (for factors that bind to narrow regions).
The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
These counts are then sorted according to their rank and the cumulative sum of read counts are plotted. An ideal input
with perfect uniform distribution of reads along the genome (i.e. without enrichments in open chromatin etc.) should
generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
few bins which corresponds to high, narrow enrichments seen for transcription factors.


.. image:: $PATH_TO_IMAGES/QC_fingerprint.png


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

.. _bamFingerprint wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint


**Output files**:

- Diagnostic plot

43:c5787c91cab8

<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.4">
    <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">bamFingerprint</token>

          #end if
      #else
        --plotFileFormat 'png'
      #end if

      #if str($region).strip() != '':
          --region '$region'
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
        --binSize '$advancedOpt.binSize'
        --numberOfSamples '$advancedOpt.numberOfSamples'

    </outputs>
    <help>

**What it does**

This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal)
and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).

The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads
along the genome (i.e. without enrichments in open chromatin etc.) should
generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
few bins which corresponds to high, narrow enrichments seen for transcription factors.


.. image:: $PATH_TO_IMAGES/QC_fingerprint.png


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


**Output files**:

- Diagnostic plot