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  • RNAseq from patients

    Hello,
    I have a question, If I have 10 Bam files (RNAseq) from 10 different patients and I want to see the different expression of few genes, what is the best tool to use after counting the reads?

    Thank you

  • #2
    featureCounts part of Subread package. You can feed all your BAM files at the same time to get a matrix of counts (rows as genes and columns as your samples).

    Comment


    • #3
      Thank you genoMax for your answer,

      can you tell me how this reads are normalized?

      thanks

      Comment


      • #4
        You will get raw counts from featureCounts. You will need to use DESeq2/edgeR etc to actually do normalization and analysis.

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        • #5
          but if I use Deseq2 it requires biological replicates, which I don't have it in my case.

          How can I create the data frame and the condition with DESq2 in this case?

          thank you
          Last edited by NDUFB11; 03-05-2019, 09:03 AM.

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          • #6
            You can use DESeq2 without replicates. It is not recommended. Your analysis would not have any statistical significance.

            Hopefully you have some other condition that you could test on?

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