comparison plotFingerprint.xml @ 4:30481ee59a46 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11

3:1bc005b195af

    </tests>
    <help>
<![CDATA[


**What it does**

This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
and is based on a method described in 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 the 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) with a uniform distribution of reads alignments
result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
most commonly seen with transcription factors.


.. image:: $PATH_TO_IMAGES/QC_fingerprint.png


You can find more details on the plotFingerprint doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotFingerprint.html


**Output files**:

- Diagnostic plot
- (optional) Data matrix of raw counts

**Output with test dataset**:

What follows is the output of plotFingerprint with our test ChIP-Seq datasets, limiting analysis to chromosome X. Single-end reads were extended to
200 bp (advanced options).

.. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png


-----

@REFERENCES@
]]>

4:30481ee59a46

    </tests>
    <help>
<![CDATA[


What it does
---------------

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


Output
---------

The default output is a diagnostic plot (see below for an example and further down for some background information).

Optionally, you can obtain the table of raw counts that was used to generate the plot.

.. image:: $PATH_TO_IMAGES/plotFingerprint_output.png
  :width: 600
  :height: 395


Example plot
-------------

What follows is the output of ``plotFingerprint`` with our test ChIP-Seq data sets, limiting the analysis to chromosome X. Single-end reads were extended to
200 bp (advanced options).

.. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
   :width: 600
   :height: 450

-----------------------------

Background
--------------

The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the 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) with a uniform distribution of reads alignments
result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
most commonly seen with transcription factors.


.. image:: $PATH_TO_IMAGES/QC_fingerprint.png
   :width: 600
   :height: 294

-----

@REFERENCES@
]]>