Intron Annotations C. Elegans

[virg4l]

I'm working with a mRNA-seq data set where I expect to find non-WT expression that includes bits of introns in mature transcripts. I'd like to be able to use HTSeq-count to add up hits in introns, but my Ensembl GTF (from Illumina's C. elegans iGenomes page) doesn't have introns as a class of annotation.

Does anyone have suggestions about where I can find such a file (or how to generate one)?

[dpryan]

No one bothers to put introns in annotation files, since the exons are already there and the introns are just between them. One of the more convenient methods to get bounds of introns is to just make/load the TxDb for your organism in R and use the intronsByTranscript() function in GenomicRanges. Note that you'll likely want to post-process that a bit (e.g., make disjoint intronic bins, find which intersect exons and then remove them).