Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • 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
        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.
        ...
        Yesterday, 11:10 AM
      • SEQadmin2
        Cancer Drug Resistance: The Lingering Barrier to Rising Survival
        by SEQadmin2



        Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

        There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
        07-08-2026, 05:17 AM
      • GATTACAT
        Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
        by GATTACAT
        Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
        07-01-2026, 11:43 AM
      View All

      ad_right_rmr

      Collapse

      News

      Collapse
      Topics Statistics Last Post
      New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2
      Started by SEQadmin2, Yesterday, 10:04 AM
      0 responses
      10 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      Yesterday, 10:04 AM  
      Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2
      Started by SEQadmin2, 07-08-2026, 10:08 AM
      0 responses
      9 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-08-2026, 10:08 AM  
      Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2
      Started by SEQadmin2, 07-07-2026, 11:05 AM
      0 responses
      16 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-07-2026, 11:05 AM  
      High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2
      Started by SEQadmin2, 07-02-2026, 11:08 AM
      0 responses
      31 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-02-2026, 11:08 AM  
      View All
      Working...