Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Removal of retained introns / primary transcripts from de novo RNAseq assembly

    Dear all,

    I have assembled a transcriptome from > 100 Mio 2x105 bp reads and obtained a nice set of sequences without a reference genome.

    Some of them are very long (> 20 kb) and a blastn/blastx search revealed that they seem to correspond to transcripts that have retained intronic sequences. [I suspect that the velvet/oases assembly is most likely correct, as unprocessed transcripts are known contaminants of polyA-selected libraries. I don't have a reference genome to proof it, though.]

    Still, I was wondering if anybody had any idea on how to remove such primary transcript sequences from my output before translating the sequences into putative proteins ?

    Thanks for any input,
    Thomas

  • #2
    I am also trying to identify ways to parse out intron containing sequences from RNAseq data in an efficient way. The best way I can think of is to make contigs which include both intron containing and intron lacking variants, and then remove the intron containing transcripts from your sequence database.

    Unfortunately, I am yet to find a good way to do this without a reference genome.

    If you find a way to do this please let us know.

    Cheers,
    T

    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
    11 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
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X