Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • mrfox
    Senior Member
    • Aug 2010
    • 103

    Different FPKM values of cufflinks and cuffdiff

    Hi all, sorry for repeatedly posting the same question. But I am still confused about the different FPKM values returned by cufflinks and cuffdiff. Did I make mistakes in one of the steps? Below is how I use the package:

    1)run cufflinks on the sam files obtained by Tophat
    2)run cuffcompare on the gtf files in last step, I used UCSC known genes as the reference. And I got the stdout.combined.gtf and the tracking files as expected.
    3)using the stdout.combined.gtf obtained in 2) as reference, I run cuffdiff on the sam files of the samples and obtained the *.diff and *.tracking files.

    However, I found that for many isoforms (from isoforms.tracking), their FPKM values from the samples usually do not match those values by cufflinks from step 1). The version I used is 0.9.2.

    Could anybody help to explain this? And, what is the reason to re-assign the reads to transcript and re-estimate abundance in cuffdiff?

    I desperately look forward to your answers. Thank you all.
  • fatrabbit
    Junior Member
    • Mar 2010
    • 7

    #2
    hi, I also faced the same problem by using version 9.1. I'm trying to use version 9.3 (the latest one), and to see if it still has the problem.

    In their website, they said "This release fixes several issues that affect abundance estimation and differential expression accuracy, and is strongly recommended for all users."

    If you have any updates, please let me know. Thanks.
    Last edited by fatrabbit; 01-11-2011, 01:01 PM.

    Comment

    • Robby
      Member
      • Mar 2011
      • 68

      #3
      Hi all, I use version 9.3, but I still have different FPKM values returned by cufflinks and cuffdiff. Did anybody observe similar problems? Has anybody tested, which results are more trustable?

      Please let me know, if somebody has any updates or recommendations. Thank you all.

      Comment

      • mrfox
        Senior Member
        • Aug 2010
        • 103

        #4
        Hi all, I used v9.3 now and cufflinks and cuffdiff generate consistent values.

        Comment

        • Robby
          Member
          • Mar 2011
          • 68

          #5
          Thanks for the fast reply, mrfox.

          Maybe I do something wrong. I did the following:
          1. cufflinks -G ucsc-reference.gtf sample_n.bam (for all samples)
          2. cuffdiff ucsc-reference.gtf sample_1.bam sample_2.bam [....] sample_n.bam
          3. compare genes.expr (cufflinks) with genes.fpkm_tracking (cuffdiff)

          @mrfox: Which values did you compare with each other? Did you perform the same steps described above?

          Comment

          • IBseq
            Member
            • Jul 2012
            • 56

            #6
            hi robby, not sure if you sorted out but I write it anyway...

            "Maybe I do something wrong. I did the following:
            1. cufflinks -G ucsc-reference.gtf sample_n.bam (for all samples)
            2. cuffdiff ucsc-reference.gtf sample_1.bam sample_2.bam [....] sample_n.bam
            3. compare genes.expr (cufflinks) with genes.fpkm_tracking (cuffdiff)
            "

            you run cufflinks correctly, but then you need to run cuffcompare and then use the output of cuffcompare to run cuffdiff to which you will provide as well the sam/.bam files from tophat...

            hope it helps,
            ib

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Pathogen Surveillance with Advanced Genomic Tools
              by seqadmin




              The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
              03-24-2025, 11:48 AM
            • seqadmin
              New Genomics Tools and Methods Shared at AGBT 2025
              by seqadmin


              This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

              The Headliner
              The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
              03-03-2025, 01:39 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-20-2025, 05:03 AM
            0 responses
            41 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-19-2025, 07:27 AM
            0 responses
            51 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-18-2025, 12:50 PM
            0 responses
            38 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-03-2025, 01:15 PM
            0 responses
            193 views
            0 reactions
            Last Post seqadmin  
            Working...