2.6 years ago by
Australia/Melbourne/University of Melbourne
Keep in mind - when you perform a cross strand correlation analysis to assess peak quality in your data, if you do not exclude blacklisted reads prior to this analysis (which generally uses aligned reads or bed converted intervals from these reads), then you will include these regions in your analysis which may skew the results one way or the other.
Devon is right - the time savings will be nice to call peaks without this step and peak calling shouldn't really be affected much by these regions, depending on which peak caller you decide to use.
Just have a look at a few of the blacklisted regions after your alignment to see what kind of signal you're getting there, and then choose whether to use filtered alignment files or not for whichever downstream analyses (following Sukhdeep Singh's suggestion).