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Old 07-03-2013, 12:28 PM   #1
bjchen
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Location: New York

Join Date: Jan 2012
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Default interpret GC bias metrics from Picard

Hi,

I am working with a RNA-seq dataset (human samples), and am generating many "metrics" from Picard to check quality. Picard has a tool "CollectGCBiasMetrics", which calculate the normalized coverage for each GC% bin. According to the manual, the normalized coverage is compared to overall coverage (which is 1). My question is, how does one interpret the normalized coverage? That is, what should we expect? What's the reasonable range for this metric? I appreciate any input!

Thanks!
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