chipseq for mitochondrial genes

mathew · 03-05-2013, 07:05 AM

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 · 03-12-2015, 04:33 AM

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.

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03-05-2013, 07:05 AM	#1
mathew Member Location: australia Join Date: Jan 2011 Posts: 81	chipseq for mitochondrial genes 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

03-12-2015, 04:33 AM	#2
mziemann Member Location: Australia Join Date: Aug 2010 Posts: 10	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.