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  • 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.

  • #2
    A good place to start

    Comment


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

      Woody

      Comment


      • #4
        Hi guys,

        I did 2x100 finally, and it worked pretty well

        Comment


        • #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

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