Hi,

I am trying to get the last 300 bases of each transcript in genomic ranges. However, when I resize with genomic ranges, it resizes each exon to 300 bases rather than resizing the sum of the exons to be 300 bases.

transcripts <- exonsBy(gencode, by = 'tx', use.names = T)

transcripts_neg <- transcripts[strand(transcripts) == '-']
transcripts_neg <- transcripts_neg[elementNROWS(transcripts_neg) > 0]
transcripts_pos <- transcripts[strand(transcripts) == '+']
transcripts_pos <- transcripts_pos[elementNROWS(transcripts_pos) > 0]

transcripts_neg
transcripts_neg_resized <- resize(transcripts_neg, 300, fix = 'start')

transcripts_pos
transcripts_pos_resized <- resize(transcripts_pos, 300, fix = 'end')

export(transcripts_neg_resized, '~/Desktop/transcripts_neg.bed')

Probably the most intuitive thing is to map the transcript range 1-300 to genomic coordinates and then intersect:

Something like:

threeprime <- IRanges(end=sum(width(gencode)), width=300L)
threeprime_genome <- pmapFromTranscripts(threeprime, gencode)
pintersect(gencode, threeprime_genome)