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FAQ : Ploidy - filtering, what is this ?

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  PLOIDY-filtering :

  During the analysis, the sam files containing the mapped fragments, are subjected to filtering of "blacklisted regions".
  These are generally very repeat-rich regions, which generate deep (but artifactual) signals in the data.
  These "false positive" peaks are seen in all samples, in all data types (Dnase-seq, ATAC-seq, RNA-seq, captureC),
  and if some of these regions are within the interaction region of any of the capture probes,
  convincing-looking interaction signal can result, and this may lead to false interpretation of the data.

  If you are interested in repeat-rich regions, you may wish to turn this filter off, by running the pipeline with --noPloidyFilter




Page updated by Jelena 27Sep2017