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  • RNA-seq pipeline on Ion-Proton data

    Hi I am a rookie bioinformatics who will process the rna-seq from Ion-proton(Single-ended).
    The pipeline for processing which I know until now is
    Bowtie, Tophat, Cufflinks, and cummeRbund for RNA-seq alignment, assembly, DE analysis, and .visualization.
    Any other options?
    Or What is this advantage or disadvantage of this pipeline?
    Thank you!
    Last edited by super0925; 02-14-2014, 07:38 AM.

  • #2
    you shouldn't double post (http://seqanswers.com/forums/showthread.php?t=40918)

    Comment


    • #3
      @ Jeremy :

      For super0925:

      The pipeline looks absolutely perfect for RNAseq analysis in general.
      I am not very sure of it using for Ion-proton.

      Any how, why dont you give a try of using the pipeline, you do get some idea & info. from the analysis, Right.

      So,go ahead, Keep posted what happens for Ion-proton RNA data.

      Comment


      • #4
        A scientist I work with recommends STAR + Bowtie 2 for RNASeq on Proton instead of TopHat. I don't think I can post a link since it's related to my job, but if you're interested in reading her poster, google "Proton RNASeq alignment", & you should find her blog post.

        Comment


        • #5
          Originally posted by jfostel View Post
          A scientist I work with recommends STAR + Bowtie 2 for RNASeq on Proton instead of TopHat. I don't think I can post a link since it's related to my job, but if you're interested in reading her poster, google "Proton RNASeq alignment", & you should find her blog post.
          I found it , it seems cool!

          Comment

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