I have aligned ChIP-Seq data to the mm10 genome, called peaks and now I want to remove the blacklisted regions.
However, the blacklist bed file provided by ENCODE is for the mm9 genome. Would it be sensible to use this file or do you think that co-ordinates might be shifted and ultimately will remove non-blacklisted regions from my datasets?
If not, is there a way to find the actual blacklisted regions for mm10?
In the end, I could align to the mm9 but I prefer using the latest genome annotation