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  • vivek_
    replied
    Splice aware aligners take into account the splice junctions between exons in gene regions while aligning RNA-seq reads. So if a read spans the splice junction on either side, it gets aligned as such.

    In ungapped alignment, the splice junction would indicate only a partial match for the reads that span these junctions and it might not be aligned.

    Leave a comment:


  • What is the diff between spliced alignment and ungapped alignment?

    Joined a workshop recently. They are talking about the RNA Seq which is not my territory. Lack of knowledge on this field.

    So any diff between those two? Thanks

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