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  • Mirna expression analysis

    Hi !

    I am pretty new at this ...

    I have a merged bam file of about 100 patients mirna's and I would like to run an analysis to determine whether there are mirna's the have higher expression than others...

    I've heard about Degseq, EdgeR and cufdiff but since I am not familiar with expression analysis I am not sure what is best for me to use.

    Can someone suggest some kind of pipeline of working with bam files in order to determine the expression?

    Thanks!

  • #2
    Hello,

    GenePattern provides a suite of RNAseq modules as well as differential expression modules which may provide an answer to your question.

    So that we may better suggest tools for you, can you provide a few more details regarding the sort of expression analysis you would like to do?

    Best

    Barbara Hill
    Cancer Informatics Development
    Broad Institute of Harvard and MIT
    Cambridge, MA
    Barbara Hill
    Software Test Engineer
    Cancer Informatics Development
    Broad Institute of Harvard and MIT
    Cambridge, MA
    USA

    Comment


    • #3
      Thanks for your answer, I will take a look at this.

      I would like to test mirna expression in a set of cancer patients ...

      Comment


      • #4
        Thanks for your answer, I will take a look at this.

        I would like to test mirna expression in a set of cancer patients ...

        Comment

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