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  • Identifying intron sequences in de novo assembled transcripts?

    Greetings!

    We're using Trinity to do de novo assembly of frog RNA-seq data. From the resulting assemblies, I'd like to be able to identify any transcripts that contain intronic sequences (from partially-spliced transcripts) so that we can filter these out of our data set. Does anyone know of a program that might do this? It would not be a problem for me to put together sets of sequences that represent introns, coding exons, and non-coding exons, in case I need to train a program, e.g. a gene predictor. I fear that predictors will not work well or at all on sequences that are the size of transcripts.

    Thanks,
    Bob

  • #2
    If your RNAseq data is produced with poly-A enrichment, the sequence should be all exons, regardless coding or non-coding. How to define the intron region for this conditioin?

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    • #3
      In theory, this is true. However, RNA-seq is so sensitive that it is likely one is also capturing pre-spliced and partially spliced mRNAs, although in very low %s. These species of molecules are the ones I'm trying to identify and remove.

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