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Intron retention was quantified by our in-house program (intron_retention_utils, https://github.com/friend1ws/intron_retention_utils) as in the previous study5. For each exon-intron boundary registered in RefSeq database, the number of presumed intron retention reads (those spanning ≥10 bp of both sides of the boundary), as well as that of normally spliced reads covering the last exonic base of the boundary, was counted.
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