Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • zinky
    Member
    • Dec 2011
    • 48

    #1

    RNA-seq depth for lncRNA quantification

    HI, guys , i have 6 human cell samples preparing for RNA-seq to do mRNA expression and lncRNA expression meta-analysis. However, i am not sure how many reads or depth are enough to my analysis.
    Someone told me that, for lncRNA analysis, there must be at least 9-10G raw data (PE100) by sequencing total RNA (only rRNA were removed). An alternative strategy is just sequencing the ployA enriched RNAs ,of which data volume should be at least 5G relatively (PE100).
    Indeed, I just want perform an expression analysis without novel lncRNA detection, so I think the SE50 can be suitable for quatifing those known lncRNA transcripts. Could anyone can make me know the minimum reads number or depth to do this work by SE50 in either strategy mentioned above.
    Many thanks!
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Genohub has a guide available (https://genohub.com/next-generation-sequencing-guide/). Look for depth of coverage for RNA. Though the guide does not specifically address lncRNA it should give you some points to consider.

    Comment

    • zinky
      Member
      • Dec 2011
      • 48

      #3
      Originally posted by GenoMax View Post
      Genohub has a guide available (https://genohub.com/next-generation-sequencing-guide/). Look for depth of coverage for RNA. Though the guide does not specifically address lncRNA it should give you some points to consider.
      thanks a lot, i also browsed this page http://www.rna-seqblog.com/how-many-reads-are-enough/, which both makes me a little clear now.

      Comment

      Latest Articles

      Collapse

      • SEQadmin2
        Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
        by SEQadmin2



        Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

        Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
        ...
        10-14-2026, 09:55 AM
      • SEQadmin2
        New Genomics Technologies Take Aim at Long-Standing Limits
        by SEQadmin2


        Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

        We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
        ...
        09-28-2026, 10:25 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by SEQadmin2, Yesterday, 11:13 AM
      0 responses
      16 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, Yesterday, 10:48 AM
      0 responses
      16 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-15-2026, 10:52 AM
      0 responses
      35 views
      0 reactions
      Last Post SEQadmin2  
      Started by SEQadmin2, 10-14-2026, 05:39 AM
      0 responses
      42 views
      0 reactions
      Last Post SEQadmin2  
      Working...