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Old 07-10-2012, 12:44 PM   #1
floydian_slip
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Default Normalization of small RNA data for library size

Hi,
I have a few libraries of small RNA reads with different read counts: some libraries have more than 10 million reads, some others have <1 million. I wanted to normalize them for their sizes only (at this point). I was wondering if Reads per Million (or RPM) would be a good choice:

RPM = (# of reads mapped)/(#of reads in millions in the library).

However, this would be one quantity for the entire library. I can then multiply it with the read count at each location to get the normalized read count (or expression). Would this be a good choice?

If you have a better choice/approach/tool, please let me know.
Thanks,
Nitin
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library size, ngs data, normalization, small rna-seq

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