comparison bamFingerprint.xml @ 8:ab153e5b5428 draft default tip

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

7:b97024fb9c9f

                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param argument="--binSize" type="integer" value="500" min="1"
                   label="Bin size in bp"
                   help="Length in base pairs for a window used to sample the genome."/>
                <param argument="--numberOfSamples" type="integer" value="100000" min="1"
                   label="Number of samples"
                   help="Number of samples taken from the genome to compute the scaling factors."/>
                <expand macro="read_processing_options" />
                <expand macro="skipZeros" />

<![CDATA[


**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

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

**Output with test dataset**:

Following is the output of bamFingerPrint 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

8:ab153e5b5428

                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param argument="--binSize" type="integer" value="500" min="1"
                   label="Bin size in bases"
                   help="Length in bases for a window used to sample the genome."/>
                <param argument="--numberOfSamples" type="integer" value="100000" min="1"
                   label="Number of samples"
                   help="Number of samples taken from the genome to compute the scaling factors."/>
                <expand macro="read_processing_options" />
                <expand macro="skipZeros" />

<![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

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

**Output with test dataset**:

What follows is the output of bamFingerPrint 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