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  • repinementer
    Member
    • Dec 2009
    • 80
    #1

    how to check the quality of RNASEQ data

    Hi guys I just started RNASEQ analysis. Seems so much going on here! :P. Lot's to catch up!
    I have currently ABI Solid RNASEQ sequencing results with me. Would you please tell me what are the basic things to done first.

    I'm thinking to check the quality of tags first
    and then use BOWTIE and TOPHAT and CUFFLINKS ?

    Thanx a tone who ever answer my naive question
    Tags: None
    • repinementer
      Member
      • Dec 2009
      • 80
      #2
      sorry for naive question

      Sorry some one already had a nice discussion in this site.
      Awesome!!!! This is the order but I don't have any answer for 1st step?

      1. normalize reads [ used ? ]
      2. map reads back to genome [Tophat-Bowtie]
      3. measure expression [ RPKM (DEGSeq) or FPKM measurement (CuffLinks) ]
      4. find differential expression [DeSeq, DEGSeq, CuffLinks]

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