Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • Boel
    Member
    • Oct 2009
    • 62
    #1

    cuffcompare - FPKM==0

    Dear All,

    I'm playing around with cufflinks, and just realized that most of my FPKM values are zero in my .tmap files although the confidence interval is != 0.

    > grep TCONS_00000051 transcripts.tmap
    USP14 TCONS_00000051 i CUFF.167867 CUFF.167867.0 100 0.000000 2.633003 13.165017 6.534247 146 CUFF.167867.0
    USP14 TCONS_00000051 i CUFF.167870 CUFF.167870.0 100 0.000000 2.309612 13.461403 6.523077 130 CUFF.167870.0
    USP14 TCONS_00000051 i CUFF.167873 CUFF.167873.0 100 0.000000 1.684046 12.115592 5.300000 130 CUFF.167873.0
    USP14 TCONS_00000051 i CUFF.167876 CUFF.167876.0 100 0.000000 44.074354 96.153772 29.000000 53 CUFF.167876.0
    USP14 TCONS_00000051 i CUFF.167879 CUFF.167879.0 100 0.000000 8.646888 24.069578 13.531915 141 CUFF.167879.0
    USP14 TCONS_00000051 i CUFF.167882 CUFF.167882.0 100 0.000000 28.206807 50.772252 32.666667 159 CUFF.167882.0
    USP14 TCONS_00000051 i CUFF.167885 CUFF.167885.0 100 0.000000 10.328430 17.438920 11.484902 563 CUFF.167885.0
    USP14 TCONS_00000051 i CUFF.167888 CUFF.167888.0 100 0.000000 9.756814 22.765900 13.182741 197 CUFF.167888.0
    USP14 TCONS_00000051 i CUFF.167891 CUFF.167891.0 100 0.000000 25.562775 42.429610 27.689796 245 CUFF.167891.0

    In the transcripts.gtf files from cufflinks all exons have FPKM values.

    This is the cuffcompare code I ran:
    cuffcompare -r /path/NCBI36.combined.gtf -R tophat_Y1_100216/transcripts.gtf tophat_Y2_100215/transcripts.gtf tophat_Y3_100216/transcripts.gtf tophat_Y4_100215/transcripts.gtf

    I'm using cufflinks-0.8.1.
    The reference gtf file (NCBI36.combined.gtf) was built from ensembl annotation (Homo_sapiens.NCBI36.48.gtf), where tss_ids were created using:
    "cuffcompare -r reference.gtf reference.gtf reference.gtf"

    Any ideas as to what might have gone wrong here?

    Thanks,
    Boel
    Tags: None
    • Ichinichi
      Member
      • Mar 2010
      • 10
      #2
      Originally posted by Boel View Post
      Dear All,

      I'm playing around with cufflinks, and just realized that most of my FPKM values are zero in my .tmap files although the confidence interval is != 0.

      > grep TCONS_00000051 transcripts.tmap
      USP14 TCONS_00000051 i CUFF.167867 CUFF.167867.0 100 0.000000 2.633003 13.165017 6.534247 146 CUFF.167867.0
      USP14 TCONS_00000051 i CUFF.167870 CUFF.167870.0 100 0.000000 2.309612 13.461403 6.523077 130 CUFF.167870.0
      USP14 TCONS_00000051 i CUFF.167873 CUFF.167873.0 100 0.000000 1.684046 12.115592 5.300000 130 CUFF.167873.0
      USP14 TCONS_00000051 i CUFF.167876 CUFF.167876.0 100 0.000000 44.074354 96.153772 29.000000 53 CUFF.167876.0
      USP14 TCONS_00000051 i CUFF.167879 CUFF.167879.0 100 0.000000 8.646888 24.069578 13.531915 141 CUFF.167879.0
      USP14 TCONS_00000051 i CUFF.167882 CUFF.167882.0 100 0.000000 28.206807 50.772252 32.666667 159 CUFF.167882.0
      USP14 TCONS_00000051 i CUFF.167885 CUFF.167885.0 100 0.000000 10.328430 17.438920 11.484902 563 CUFF.167885.0
      USP14 TCONS_00000051 i CUFF.167888 CUFF.167888.0 100 0.000000 9.756814 22.765900 13.182741 197 CUFF.167888.0
      USP14 TCONS_00000051 i CUFF.167891 CUFF.167891.0 100 0.000000 25.562775 42.429610 27.689796 245 CUFF.167891.0

      In the transcripts.gtf files from cufflinks all exons have FPKM values.

      This is the cuffcompare code I ran:
      cuffcompare -r /path/NCBI36.combined.gtf -R tophat_Y1_100216/transcripts.gtf tophat_Y2_100215/transcripts.gtf tophat_Y3_100216/transcripts.gtf tophat_Y4_100215/transcripts.gtf

      I'm using cufflinks-0.8.1.
      The reference gtf file (NCBI36.combined.gtf) was built from ensembl annotation (Homo_sapiens.NCBI36.48.gtf), where tss_ids were created using:
      "cuffcompare -r reference.gtf reference.gtf reference.gtf"

      Any ideas as to what might have gone wrong here?

      Thanks,
      Boel
      I have this exact same problem. Any help?

        Comment

        • Boel
          Member
          • Oct 2009
          • 62
          #3
          Bug

          Apparently this is a bug, and Cole & CO is currently working on solving it for the new release that should come out in the near future. Haven't heard anything more yet.

            Comment

            Previous template Next

            Latest Articles

            Collapse
            • SEQadmin2
              Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
              by SEQadmin2



              CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

              Despite this, “CRISPR helped turn genome editing from a specialized technique into              ...
              07-31-2026, 11:01 AM
            • SEQadmin2
              Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
              by SEQadmin2


              Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

              The systematic characterization of the human proteome has              ...
              07-20-2026, 11:48 AM
            • SEQadmin2
              Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
              by SEQadmin2



              Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
              ...
              07-09-2026, 11:10 AM
            View All

            ad_right_rmr

            Collapse

            News

            Collapse
            Topics Statistics Last Post
            Long-Read Sequencing Closes Decades-Old Gaps in the Medaka Genome by SEQadmin2
            Started by SEQadmin2, 08-03-2026, 10:13 AM
            0 responses
            15 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            08-03-2026, 10:13 AM  
            New Genomic Method Uncovers Ancient Hominin DNA by SEQadmin2
            Started by SEQadmin2, 07-31-2026, 02:55 AM
            0 responses
            32 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            07-31-2026, 02:55 AM  
            Study Captures the First Moments of DNA Replication by SEQadmin2
            Started by SEQadmin2, 07-24-2026, 12:17 PM
            0 responses
            23 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            07-24-2026, 12:17 PM  
            Chemotherapy Leaves Detectable DNA Signatures in Childhood Tumors by SEQadmin2
            Started by SEQadmin2, 07-23-2026, 11:41 AM
            0 responses
            21 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            07-23-2026, 11:41 AM  
            View All
            Working...