Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Tophat for finding long ncRNA with short reads?

    Hi,
    has anyone used Tophat to look at long non coding RNAs or mRNA like ncRNAs using NGS?

    I am assuming of course that things would be easier if I had 454 or even Sanger reads. But Solexa and SOLiD would be more bang for the buck.

    aside from de novo assembly of the transcriptome. I am wondering if it is possible to use Tophat / Cufflinks to generate the transcripts
    http://kevin-gattaca.blogspot.com/

  • #2
    I actually discovered an interesting ncRNA using the tophat-->cufflinks-->cuffcompare-->cudffdiff pipeline.

    I map my reads to the reference using tophat, then run cufflinks without providing a reference gtf file. Following that I run cuffcompare where I do provide the reference gtf file and finally cuffdiff. I then screened through the significant cuffdiff results looking at the loci with no corresponding gene name entry from the reference gtf and tried to classify these. One is clearly a novel sRNA loci that has previously not been described and certainly not in the trait that my different samples come from.

    So, in summary, it seems to work.

    Comment


    • #3
      grouping small rna dataset into long RNA clusters

      You can try to group your small rna dataset into long RNA clusters using methods described in our deepBase ( http://deepbase.sysu.edu.cn/ ) (Yang et al. Nucleic Acids Res. 2010 Jan;38: D123-D130.).

      we have identified ~1.2 million long RNA clusters by grouping all the mapped small RNA reads according to their distance in our deepBase platform ( http://deepbase.sysu.edu.cn/ ), which were developed to discover small and long ncRNAs from deep-sequencing data.

      These ~1.2 million RNA clusters that include multiple classes of infrastructural ncRNAs, miRNAs precursor, piRNA precursors, repeat-associated siRNA precursors and evolutionarily conserved phastCons elements.

      we have identified ~2000 microRNA candidates and ~1890 snoRNA candidates using improved miRDeep and our snoSeeker programs from these RNA clusters.

      Comment


      • #4
        Hello everyone
        I hv rnaseq data but reference genome is not available.I want to predict lncRNA from rnaseq data. Pls give ur valuable suggestions.

        Comment

        Latest Articles

        Collapse

        • 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
        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-14-2024, 06:13 AM
        0 responses
        34 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-08-2024, 08:03 AM
        0 responses
        72 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-07-2024, 08:13 AM
        0 responses
        81 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-06-2024, 09:51 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X