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  • 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

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