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I am looking for a easy way to calculate the intervals of flanking introns based on a transcript annotation file. I have chosen a very complicated method:

bedtools subtract -s -a genes.bed -b onlyExons.bed > introns_hg38.bed

Then I calculated the start and end positions of the transcripts from transcript.gtf annotation file and searched for adjacent intron intervals in R. Unfortunately I don't find all the flanking introns. Perhaps this is due to the 3'UTR or 5'UTR or other sequences that are not introns or exons. Any suggestions?

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