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  • Bowtie and Cufflinks

    Hello,

    I have aligned Solexa sequencing data using Bowtie and plan on creating expression profiles using Cufflinks by looking at RPKM values.

    There is one thing I am curious about. Is there a way to compare your alignments to annotated regions, so you can give the reads a name along with an RPKM value? I'm assuming Cufflinks simply gives you a read and it's RPKM, what I would like is to be able to see X gene, X miRNA, X puesdogene has an RPKM value of Y.

    Is there a way to make this possible? Any suggestions would be great.


    Thanks,
    Brandon

  • #2
    Cufflinks will give you a gene/transcript and its RPKM (if you feed it a gff file). If you don't, it will give you a "made up" gene/transcript and its RPKM.

    RPKM is always in terms of a larger genomic entity, not a single read. Reads per kilobase per million.

    Hi, fellow Kansas Citian!

    Comment


    • #3
      mgogol, thank you for the reply.

      Do you work in bioinformatics here in the Kansas City area? I work at UMKC.

      Comment


      • #4
        Yep, I'm at Stowers.

        Comment


        • #5
          I'm at KU Med... Looks like KC is representing well.

          Comment


          • #6
            I've seen your name around the forum... I went to KU, so it jumped out at me.

            Comment


            • #7
              We should all get together sometime for lunch. It would be nice to talk face to face with others that actually understand what you are doing.

              Comment


              • #8
                I emailed you...

                Comment


                • #9
                  Kansas City seems to be well represented here.

                  Comment

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