Using a genome subset
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A genome subset can be given as an optional parameter to compute the enrichment only on a subset of the genome. For instance, we might interest ourself only on the neighborhood of transcription start sites (TSS). Therefore, a bed file containing these regions can be provided through the **--genome_subset** parameter.

.. image:: ../images/fig5.jpg

The genome subset will therefore induce a subset of TE database, and a subset of each input bed files. Then, the genome size is re-calculated based on the total number of base pair included in genome_subset bed file.

Default genome subset
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The default genome subset is the mappable regions according to `UCSC mappability track <https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=mappability>`_. We use any sequence with non-zero mappability as our default genome subset (therefore any inputs or TEs falling inside it are ignored).