Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • RNA Star with and without GFF problems

    Actually, I am having a lot of problems with this particular analysis, but lets start with this. I have some good RNA, deep read count, triplicate biological replicate data from Drosophila heads - small genome and well annotated. SHould be easy, right?

    I have tried the Ensamble and Flybase files for mapping with various results. Most important is that for Flybase I can't seem to get any GFF3 or GTF files to work with the Fasta file using RNA Star (in Galaxy). For the Ensemble data, I can get them both to work, but in the end I get very few significant hits - but I already know some of our previous analysis - which I won't get into - revealed differentially expressed transcripts that we showed by both qRT-PCR and proteomic analysis are real - i.e. I believe them more than any bioinformatic proof.

    Here is the Ensemble repository I used Ensemble FTP

    Here is the Flybase repository I used Flybase FTP

    Table of RNA Star Mapping Trials

    Any help appreciated. Trying to do both CufDiff and DEseq analysis on this data.

  • #2
    Hi tonup69,

    Might be best to post the actual error you are getting - why won't RNA Star accept your files?

    Cheers,

    Matt.

    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
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X