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  • How to create count table for SOAP output?

    Hi
    I would like to use SOAP to align RNA-Seq reads with Rice genome, i have 2 questions :

    1- How can i use GTF gene annotation file in SOAP ? (and which version?)
    2-How can i create Count table for SOAP output (any software) ?

    thanks

  • #2
    Soap is not designed for RNA-seq alignment, and it does not use GTF files. You'd be better off using a splice-aware aligner such as BBMap, TopHat, or Star.

    For determining gene expression, many people use Cufflinks.

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