Header Leaderboard Ad

Collapse

Empty FPKM estimates after cuffcompare

Collapse

Announcement

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

  • Empty FPKM estimates after cuffcompare

    I ran cufflinks on several BAM files and get tracking.gtf files looking like (truncated lines):

    Code:
    Chr1    Cufflinks   transcript  22746   23685   1000    +   .   gene_id "CUFF.8"; transcript_id "CUFF.8.1"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "52.362831";
    Chr1    Cufflinks   exon    22746   23020   1000    +   .   gene_id "CUFF.8"; transcript_id "CUFF.8.1"; exon_number "1"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "$
    Chr1    Cufflinks   exon    23096   23685   1000    +   .   gene_id "CUFF.8"; transcript_id "CUFF.8.1"; exon_number "2"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "$
    Chr1    Cufflinks   transcript  79944   80186   1000    +   .   gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "3077.9273423595"; frac "1.000000"; conf_lo "1765.494714"; conf_hi "4390.359971"; cov "2714.84$
    Ch
    and then run cuffcompare to compare with a merged gtf file as
    Code:
    cuffcompare -o myprefix -r merged.gtf transcripts.gtf
    but, the myprefix.tracking only gives me FPKM estimates equal zero for all genes:

    Code:
    TCONS_00000001  XLOC_000001 XLOC_000001|TCONS_00000001  c   q1:CUFF.8|CUFF.8.1|100|0.000000|0.000000|0.000000|0.000000|-
    TCONS_00000002  XLOC_000002 XLOC_000002|TCONS_00000002  =   q1:CUFF.11|CUFF.11.1|100|0.000000|0.000000|0.000000|0.000000|-
    TCONS_00000003  XLOC_000003 XLOC_000003|TCONS_00000003  =   q1:CUFF.2|CUFF.2.1|100|0.000000|0.000000|0.000000|0.000000|-
    TCONS_00000004  XLOC_000004 XLOC_000004|TCONS_00000004  =   q1:CUFF.4|CUFF.4.1|100|0.000000|0.000000|0.000000|0.000000|-
    TCONS_00000005  XLOC_000005 XLOC_000005|TCONS_00000006  c   q1:CUFF.16|CUFF.16.1|100|0.000000|0.000000|0.000000|0.000000|-
    T
    note that CUFF.8 in the transcripts.gtf has a non-zero FPKM estimate but this does not propagate to the myprefix.tracking file.

    Any ideas why? Grateful for answers.

  • #2
    Have you tried running it with Cufflinks-1.1.0? (released last week)

    I noticed a similar problem with the .tmap files generated by cuffcompare in release 1.0.3, however that problem seems to have been corrected in the most recent release.

    Comment


    • #3
      Thanks for the tip, I tried Cufflinks-1.1.0 and indeed this solves the problem!

      Comment

      Latest Articles

      Collapse

      • seqadmin
        How RNA-Seq is Transforming Cancer Studies
        by seqadmin



        Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...
        09-07-2023, 11:15 PM
      • seqadmin
        Methods for Investigating the Transcriptome
        by seqadmin




        Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.

        Whole Transcriptome RNA-seq
        Whole transcriptome sequencing...
        08-31-2023, 11:07 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 07:42 AM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-22-2023, 09:05 AM
      0 responses
      23 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-21-2023, 06:18 AM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-20-2023, 09:17 AM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Working...
      X