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Bowtie and Human transcripts



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  • Bowtie and Human transcripts

    Hallo Bowtie user,

    I have a dateset with all transcripts from human genome. On the other side I have a set of RNA-seq reads (mate pairs/Illumina).
    I would like to map these reads against the transcripts. .

    I was thinking of using bowtie to accomplish this task, but I am not
    very sure about which options or flags I should use. I thought, I have to map my reads using the bowtie option -norc. I have already tried this,
    but I am not sure, if It is the rigth one.
    Do you think, that these are the wrigth options to run bowtie for this task?
    Thanks in advance

  • #2
    Check out tophat, that uses bowtie for rna seq reads. Maybe you can find the flags and parameters for bowtie from tophat manual


    • #3
      Originally posted by bioinfosm View Post
      Check out tophat, that uses bowtie for rna seq reads. Maybe you can find the flags and parameters for bowtie from tophat manual
      I second that. Take a look at TopHat.



      • #4
        Thanks for the answers.
        The problem is that I dont want to map my reads against the whole genome,but I want to map them only against the transcript sequences (which contain already both sense and antisense transcripts). So I have already have the splice junctions in my transripts.
        But I am not sure, if I should allow the bowtie to reverse my transcript sequences or not and how to handle the mate-pairs?


        • #5
          Hi Merfer,

          I am also in your situation I want to quantify the gene expression. How to do that? Where did you get the human genome transcripts? please suggest me.

          Thanks in advance,


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