Select mm10 in the drop-down box
The ATAC-seq authors recently created a mitochondrial blacklist (found here) for use on ATAC-seq data which represents high signal regions on the nuclear genome caused by read sequence homology with the mitochondrial genome. A signal artifact blackist has also been created by ENCODE (found here).
In the command line:
for i in *.bedfile; do bedtools intersect -v -a $i -b [PATH]/mitochondrial.blacklist.bed [PATH]/signal.artifact.blacklist.bed > $i.bed; done
Be careful to not create an infinite loop with this command (all the files may end in .bed)
Probably you are looking for this