IGV showing RNA-Seq coverage of only a single exon of a gene

Question

[nucleotideaware]

I've been exploring some STAR-aligned tumor RNA-Seq data in IGV, and noticed that coverage for either of the two reference coding transcripts of one particular gene (per Ensembl) is low throughout (e.g. some exons with 2 reads, some with 0) except for ~100 depth for one exon at the end of the gene.

Any thoughts on how I should interpret and further analyze this? Is this likely to be due to bias in the sequencing or is it suggesting that only that particular exon is expressed?

Relatedly, when I run Kallisto using --genomebam and view the pseudoalignments in IGV, I see a similar distribution except the depths below these exons are multiplied by an order of magnitude (thousands instead of ~100 reads overlapping that final exon). I'm trying to figure out that order of magnitude difference.

I'd appreciate any insight into either of the above questions. Thanks so much!

[swbarnes2]

What library prep kit was used? There are 3' biased libraries which would result in what you see.

[nucleotideaware]

Thank you, that's a great point -- I'm not sure about the library prep, yet. I do see that Picard's MEDIAN_3PRIME_BIAS is 0.85 and MEDIAN_5PRIME_TO_3PRIME_BIAS is 0.08, and if I'm interpreting these metrics correctly the latter seems to confirm 3' bias throughout.