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  • Running cufflinks

    Hi,

    I have a doubt regarding running cufflinks. i have to seperate tophat
    output i need to get combined cufflinks result for this two tophat
    outputs. i ran

    cufflinks accepted_hits_1.bam accepted_hits_2.bam -o output

    Or should i do by concatenating two output files from tophat and run for a
    consolidated file.??

    Will this make a difference.?
    Please help.??
    Thank you in advance.

    Deepak

  • #2
    Hi Deepak,

    I don't quite understand what you need to do. Can you be a bit more clear? If you need to get a combined cufflinks result what you can do is the following,

    cufflinks -o output -G (reference file) accepted_hits.bam accepted_hits.bam

    Hope this helps,

    Comment


    • #3
      The cuffmerge tool is used for merging cufflinks output from numerous bam files. Have you tried that?

      Comment


      • #4
        Hi,

        @Kaustubh: i have done the same as you suggested. i just want an assurance that it will work fine.
        @pbluescript: No i havent tried cuffmerge. Can you please help me how to do it..??

        Comment


        • #5
          Originally posted by oxydeepu View Post
          Hi,

          @Kaustubh: i have done the same as you suggested. i just want an assurance that it will work fine.
          @pbluescript: No i havent tried cuffmerge. Can you please help me how to do it..??
          Not much to it really. Check out the manual:

          Comment

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