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  • RNA-seq depth/plant

    Hi everybody!
    I'm a beginner in this subject and I have a doubt about the numbers of reads / coverage necessary for plant mRNA sequencing. I would like to sequence mRNA from apical meristems of a tree inoculated and non-inoculated with a pathogen, in order to identify the differential expression. No reference genome is available. I'm planning to perform 1x100 pb (illumina Hiseq) for each sample. According to the service provider they can guarantee 5-7.5 millions of reads per 10% channel. I wonder if it is enough for each sample. Where can I get some theoretical material about this issue? Thank you very much.

  • #2
    Ideally for doing DE you would need 10 million reads per replicate. However you can still do it with 5-7.5 million reads. I don't understand what do you mean by 10% channel. Could you explain that? Also without reference genome, how are you going to map your reads? Do you have closely related genome sequence available?

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    • #3
      10% of a "channel" probably means 10% of a lane.

      For a de novo transcriptome sequence you might want to use PE reads since they can aid in assembly.

      --
      Phillip

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      • #4
        thanks puendra and Phillip.
        I have a closely related genome available. The service provider used this term "10% per channel". I understood as Phillip explained.

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