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  • Gapped alignment with RNA-Seq

    It seems that the mainstream tools used for RNA-Seq analysis are Tophat and Cufflinks. However, since Tophat is bowtie-based it can't do gapped alignment with short reads. I thought of mapping with BWA and using the resulting SAM with Cufflinks, but as BWA is not meant for RNA-Seq alignment I am hesitant. Does anyone know of an RNA-Seq aligner that supports gapped alignment?

  • #2
    hey,


    try QPALMA.


    it shows off some really nice result. Hope that helps.


    regards sphil

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    • #3
      I couldn't seem to find anything suggesting QPALMA solves the problem of gapped alignment. Specifically I couldn't find anything about gapped alignments in vmatch which QPALMA uses.

      Am I not mistaken?

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