Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • FPKM = RPKM for single end reads?

    Hi Readers,

    I am a computer scientist and I am trying to understand the relationship between RPKM and FPKM. I have read this following thread and a lot of it, the biological parts, were going past me.

    I ran an analysis using cufflinks/cuffdiff/cummeRbund on single ends read data. I have a cummerRbund scatter plot comparing biological condition A FMKM gene scores to biological condition B FPKM gene scores. Is this right? Or am I really comparing RPKM scores here since FPKM = RPKM when I have single reads?

    If I am wrong, can someone please explain to me why they are not equivalent mathematically when given single end reads?

    Thanks,
    GeekyOmega

  • #2
    Yes, FPKM==RPKM for single-end reads.

    Comment


    • #3
      My understanding is that FPKM (as defined by cufflinks) approximates RPKM, but is not the same because cufflinks will distribute hits mapped to multiple transcripts across those transcripts based on the expected isoform frequencies (or possibly equally distributed).

      Comment


      • #4
        FPKM will only approximate RPKM for paired-end reads, it will be identical for single-end reads.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Essential Discoveries and Tools in Epitranscriptomics
          by seqadmin


          The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
          Yesterday, 07:01 AM
        • seqadmin
          Current Approaches to Protein Sequencing
          by seqadmin


          Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
          04-04-2024, 04:25 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 04-11-2024, 12:08 PM
        0 responses
        39 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        41 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        35 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        55 views
        0 likes
        Last Post seqadmin  
        Working...
        X