chipseq for mitochondrial genes

[mathew]

I have a dataset where chipseq was performed and I am looking specifically for mitochondrial genes. Is there a special work flow which I may use or normal BWa aligners should be used and follow the regular approach of calling peaks with MACS or SICER.

Thanks

[mziemann]

Use a standard ChIP-seq pipeline which includes binning the genome or peakfinding followed by differential expression with edgeR or DESeq then search through those results located on chrM or MT.