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Old 03-05-2013, 07:05 AM   #1
Location: australia

Join Date: Jan 2011
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Default 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.

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Old 03-12-2015, 04:33 AM   #2
Location: Australia

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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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