Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • NicoBxl
    not just another member
    • Aug 2010
    • 264

    RNA-seq sequencing depth

    Hi everybody,

    I've several questions about sequencing depth and RNA-seq. So, what is the minimal read count (in the raw data) to have a good view of :

    1. gene expression ?
    2. Differential splicing ?
    3. Low expressed transcripts (like lncRNA) ?
    4. Fusion gene ?

    I read that 100M is a minimum for fusion gene ? Is that correct ?
    I want to do 2x50bp strand-specific libraires and sequenced them on a HiSeq 2000. Is 50bp enough to find accurately fusion gene ?

    Thanks,

    N.
  • TonyBrooks
    Senior Member
    • Jun 2009
    • 303

    #2
    A good place to start

    Comment

    • woodydon
      Member
      • Jan 2010
      • 52

      #3
      50 bp is not enough. You should try 200bp or longer.

      Woody

      Comment

      • NicoBxl
        not just another member
        • Aug 2010
        • 264

        #4
        Hi guys,

        I did 2x100 finally, and it worked pretty well

        Comment

        • puggie
          Member
          • Nov 2011
          • 52

          #5
          I'm glad it work out for you Depending on what you are looking for depth is something to consider.

          Out of curiosity how did you sequence, i.e. reads/sample?

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Pathogen Surveillance with Advanced Genomic Tools
            by seqadmin




            The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
            03-24-2025, 11:48 AM
          • seqadmin
            New Genomics Tools and Methods Shared at AGBT 2025
            by seqadmin


            This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

            The Headliner
            The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
            03-03-2025, 01:39 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 03-20-2025, 05:03 AM
          0 responses
          49 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-19-2025, 07:27 AM
          0 responses
          57 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-18-2025, 12:50 PM
          0 responses
          50 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-03-2025, 01:15 PM
          0 responses
          200 views
          0 reactions
          Last Post seqadmin  
          Working...