Question: What the use of MEDIAN_CV_COVERAGE from picard RNA metrics
1
gravatar for pengchy
4.1 years ago by
pengchy410
China/Beijing
pengchy410 wrote:

Hi all,

I have calculated the MEDIAN_CV_COVERAGE, however, what the meaning of this measurement? I have checked the related discuss at seqanswers [1] and asked the question there. In brief, if the MEDIAN_CV_COVERAGE as the defined on wiki, the calculated value should be larger than the output of picard. In my data sets, this value just range between 0.2 and 1.7. To my understand, this value will definitely larger than 0 for normal samples. Because the coverage for high expressed genes should be very high and the variation for the top 1000 highly expressed genes will be large. Am I right?

[1] http://seqanswers.com/forums/showthread.php?t=21420&highlight=MEDIAN_CV_COVERAGE

Thank you!

Best,

p

rna-seq picard • 1.5k views
ADD COMMENTlink modified 3.9 years ago by Sean Davis25k • written 4.1 years ago by pengchy410
3
gravatar for Sean Davis
3.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

The MEDIAN_CV_COVERAGE represents a measurement of the variability of coverage over single genes.  Ideally, there would be no variation over the length of the genes, but in reality, there is always some.  Extreme outlier samples may represent technical differences in those samples that lead to higher variability.  In practice, take a look in a browser (IGV, etc.) at the extreme samples on the low and high end to get a sense of what the value represents.

ADD COMMENTlink written 3.9 years ago by Sean Davis25k

Hi Sean Davis, Thank you for your answer. I have misunderstood this for variation of expression level across genes.

I wonder how the coverage was calculated, because the value of MEDIAN_CV_COVERAGE range from 0.2 to 1.7 in my samples. I guess the coverage of one gene is calculated as the coverage CV across all positions. 

ADD REPLYlink written 3.9 years ago by pengchy410

You are correct.

ADD REPLYlink written 3.9 years ago by Sean Davis25k
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