Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • with cufflinks, can there be "0" fpkm value and yet full read support?

    Hi,
    I used hisat2 (2.0.5) to map 150b Paired-end reads on to the draft genome of castorbean and used cufflinks (version 2.2.1) to perform reference annotation based transcript assembly (RABT). This data is NOT for differential expression analysis. The assembler reported novel isoforms and some novel genes. From the results, of the transcripts that were as present in the gtf file used for RABT, some had an FPKM value of "0.0000000000" but were "yes" for "full_read_support" whereas the rest that were "yes" for "full_read_support" carried an FPKM value at 1 or above.
    Could anyone please explain why would a transcript be described as present with "full_read_support," yet with an FPKM value of "0.0000000000?"

    Thanks.

  • #2
    I have noticed similar problems with Cufflinks in the past. Our research group no longer uses it because it hasn't been updated in 3 years and some of the FPKM values look suspicious, which you have noticed.

    Comment


    • #3
      Thank you, Dario1984.
      Then, what method do you follow for the assembly of reads that do not have such limitations?

      Comment


      • #4
        We use Trinity because we found its results can be experimentally validated by biologists. There's also a genome guided assembly mode. It was developed a few years ago, but it still maintained by the developer. You might also be interested in categorising your assembled transcripts with TransDecoder.

        Comment


        • #5
          Thank you.
          I will go through the possibilities you have suggested.

          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