comparison hicAggregateContacts.xml @ 2:2abdd761461b draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7

1:ec59bf4c3d06

**hicAggregateContacts** outputs a plot of aggregated contacts.

Below, you can find an example of an aggregate Hi-C matrix obtained from *Drosophila melanogaster* Hi-C data. The interactions are plotted at binding sites of a protein that were determined by ChIP-seq. We plot sub-matrices of 30 bins (1.5 kb bin size, 45 kb in total). The regions specified in the BED file will be centered between half number of bins and the other half number of bins.The considered range is 300-1000 kb. The range should be adjusted and only contain contacts larger than TAD size to reduce background interactions.

.. image:: $PATH_TO_IMAGES/hicAggregateContacts.png

This example was calculated using mean interactions of an observed vs. expected transformed Hi-C matrix. Additional options for the matrix transformation are total-counts or z-score. Aggregate contacts can be plotted in 2D or 3D.

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2:2abdd761461b

**hicAggregateContacts** outputs a plot of aggregated contacts.

Below, you can find an example of an aggregate Hi-C matrix obtained from *Drosophila melanogaster* Hi-C data. The interactions are plotted at binding sites of a protein that were determined by ChIP-seq. We plot sub-matrices of 30 bins (1.5 kb bin size, 45 kb in total). The regions specified in the BED file will be centered between half number of bins and the other half number of bins.The considered range is 300-1000 kb. The range should be adjusted and only contain contacts larger than TAD size to reduce background interactions.

.. image:: $PATH_TO_IMAGES/hicAggregateContacts.png
   :width: 80 %

This example was calculated using mean interactions of an observed vs. expected transformed Hi-C matrix. Additional options for the matrix transformation are total-counts or z-score. Aggregate contacts can be plotted in 2D or 3D.

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