comparison bamCompare.xml @ 37:2f7edf06a5da draft

Uploaded

36:ea2f64efe70d

      #if $comparison.type=='subtract':
          #if $comparison.normalization.type=='rpkm':
            --normalizeUsingRPKM
          #elif $comparison.normalization.type=='1x':
            --normalizeTo1x $comparison.normalization.normalizeTo1x
          #end if
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
            #if $advancedOpt.smoothLength:

                        <option value="no">Do not normalize or scale</option>
                    </param>
                    <when value="rpkm" />
                    <when value="no" />
                    <when value="1x">
                        <param name="normalizeTo1x" type="integer" value="2150570000"
                            label="Report normalized coverage to 1x sequenceing depth"
                            help ="Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
                    </when>
                </conditional>
            </when>
        </conditional>

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


**Output files**:

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

-----

.. class:: infomark

    </help>
</tool>

37:2f7edf06a5da

      #if $comparison.type=='subtract':
          #if $comparison.normalization.type=='rpkm':
            --normalizeUsingRPKM
          #elif $comparison.normalization.type=='1x':

            #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
                --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
            #else:
                --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
            #end if

          #end if
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
            #if $advancedOpt.smoothLength:

                        <option value="no">Do not normalize or scale</option>
                    </param>
                    <when value="rpkm" />
                    <when value="no" />
                    <when value="1x">
                        <expand macro="effectiveGenomeSize" />
                    </when>
                </conditional>
            </when>
        </conditional>

.. 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.

-----

@REFERENCES@

    </help>
</tool>