Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • multiple lines per single gene in gene_exp.diff output of cuffdiff

    question that was posted on another forum, maybe someone here will have an answer:

    after running cuffdiff, in the gene_exp.diff file there are multiple lines for the same gene, with different FPKM values.
    any idea for the cause or how should I handle this to receive a single value per gene?

    http://seqanswers.com/forums/showthr...4650#post34650

    thanks
    Reut

  • #2
    Reut,

    Have you gone back to your something.combined.gtf file to look up the entry by XLOC value?

    I assumed that this was a bug and wrote a little program that compares the gene_exp.diff file and the combined.gtf and fixes the locus field in gene_exp.diff to what it should be based on the gtf file.

    Has anyone else had any experience with this?

    Sam

    Comment


    • #3
      Multiple entries of a gene/locus at Cuffdiff Differential Gene Expression Output

      Hi,

      I'm also getting this probelm (gene_exp.diff):

      XLOC_021564 Hnf4a 3:165976692-166162683
      XLOC_022796 Hnf4a 3:165976692-166162683
      XLOC_022797 Hnf4a 3:165976692-166162683

      When I looked at isoform_exp.diff file for Hnf4a all the mentioned isoforms like in the same region 3:165976692-166162683, but seem to be distributed among the above locus ids such that no locus id above share any isoform:
      test_id gene_id gene locus
      TCONS_00057332 XLOC_021564 Hnf4a 3:165976692-166162683
      TCONS_00057337 XLOC_021564 Hnf4a 3:165976692-166162683
      TCONS_00057338 XLOC_021564 Hnf4a 3:165976692-166162683
      TCONS_00057339 XLOC_021564 Hnf4a 3:165976692-166162683
      TCONS_00057340 XLOC_021564 Hnf4a 3:165976692-166162683
      TCONS_00057341 XLOC_021564 Hnf4a 3:165976692-166162683
      TCONS_00057342 XLOC_021564 Hnf4a 3:165976692-166162683
      TCONS_00060713 XLOC_022796 Hnf4a 3:165976692-166162683
      TCONS_00060714 XLOC_022797 Hnf4a 3:165976692-166162683
      TCONS_00060715 XLOC_022797 Hnf4a 3:165976692-166162683

      My pipeline:

      Gsnap (Reference guided Mapping, default settings) --> Remove softclip bases (script shared by rna-star author Alexander Dobin) --> Cufflinks (Reference guided; default settings) --> Cuffmerge (all samples cufflinks transcript.gtf + reference.gtf) --> Cuffdiff (default settings)

      The reason to remove soft-clip bases prior to running cufflinks is to have compatibility of Gsnap mapping output with Cufflinks because cufflinks uses soft-clipped bases to do assembly leading to assembled transcripts sometimes beyond reference length and throws an error at Cuffmerge. For more info on this


      Right now I am re-running the above pipeline with TopHat but I don't think it will solve this problem, because the problem is at cuffmerge, I think, in deciding to include some transcript/isoform assembly under one locus id and some in the other, within the same locus region, leading to redundancy in locus region and gene enteries.

      This is not for 1 gene above. Overall in gene_exp.diff file:

      Out of 25667 genes 3776 are repeated
      Out of 23862 loci positions (format: chr:start-end) 5759 are repeated.


      That's a significant number of genes have multiple entries.

      Did anyone else have this problem as well?

      Cufflinks version I used: cufflinks/2.2.1
      Genome: Rat genome rn5 (Ensembl db)
      Reference gtf of genes: Ensembl database version 77 for rn5


      Thanks,
      Rahil
      Last edited by rahilsethi; 03-09-2015, 04:29 AM.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X