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If the Require junction reads to match introns check button is selected, only junction reads that overlap with exonic regions and match the skipped bases of an intron in the transcript will be included in the calculation. Otherwise, as long as the reads overlap within the exonic region, they will be counted. Detailed information about read compatibility can be found in the Understanding Reads tutorial.

There are five options in Strand specificity drop-down selection. We recommend verifying with the data source how the NGS library was prepared to ensure correct option selection.

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