comparison bamCompare.xml @ 24:d7c9fd76e41e draft

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23:8c452f37c896

      #end if

    </command>

    <inputs>
        <param name="bamFile1" format="bam" type="data" label="Treatment BAM file"
            help="The BAM file must be sorted."/>

        <param name="bamFile2" format="bam" type="data" label="BAM file"
            help="The BAM file must be sorted."/>

        <param name="fragmentLength" type="integer" value="300" min="1"
            label="Length of the average fragment size"
            help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>

        <conditional name="scaling">
            <param name="method" type="select" 
                label="Method to use for scaling the largest sample to the smallest">
                <option value="readCount" selected="true">read count</option>
                <option value="SES">signal extraction scaling (SES)</option>
                <option value="own">enter own scaling factors</option>
            </param>
            <when value="SES">
                <param name="sampleLength" type="integer" value="1000" min="10"
                    label="Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two  BAM files "

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


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

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


**Output files**:

- same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.

24:d7c9fd76e41e

      #end if

    </command>

    <inputs>
        <param name="bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
            help="The BAM file must be sorted."/>

        <param name="bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
            help="The BAM file must be sorted."/>

        <param name="fragmentLength" type="integer" value="300" min="1"
            label="Length of the average fragment size"
            help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>

        <conditional name="scaling">
            <param name="method" type="select" 
                label="Method to use for scaling the largest sample to the smallest">
                <option value="readCount" selected="true">read count</option>
                <option value="SES">signal extraction scaling (SES), check the bamFingerprint plot before using it!</option>
                <option value="own">enter own scaling factors</option>
            </param>
            <when value="SES">
                <param name="sampleLength" type="integer" value="1000" min="10"
                    label="Length in base pairs used to sample the genome and compute the size or scaling factors to compare the two  BAM files "

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


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


**Output files**:

- same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.