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  • g781
    Member
    • May 2010
    • 25
    #1

    FPKM formula

    Hi everyone,

    About the FPKM formula, should I use the total number of paired-end reads in the raw fastq file as a normalization term or use the total number of paired-end reads with good qualities ( MAPQ>20) as a normalization term?

    Which one is usually used? The paper just mentioned the total number of reads. It seems to me the number is from raw fastq. But I would think the number of good quality paired-end reads sounds more reasonable. Can someone give me some suggestions?

    Thanks.
    Tags: None
  • dfhdfh
    Member
    • Jan 2013
    • 46
    #2
    It should be the number of reads you use for alignment, etc. These should be the ones passing your quality criteria.

    Comment

    • g781
      Member
      • May 2010
      • 25
      #3
      Hi dfhdfh

      Got it. Thank you very much.

      Comment

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