Is there a straightforward way to use RNA alignment with the genome to infer exon-intron structure?

Question

[charleslindberg976]

Hi!

I am working on a relatively obscure organism for which I have the total-RNA-seq (unspliced + spliced) transcripts and the genome. The gene annotation for the genome is a bit suspect however and contains several 'hypothetical proteins'. I want to measure the RNA counts for a specific gene, and use these to make inferences about exons and introns within the gene. The genomic region corresponds to a hypothetical protein that already has annotated exons and introns that I don't think have been inferred correctly.

Is there a straightforward way to use RNA alignment with the genome to infer exon intron structure?

[seidel]

StringTie or Cufflinks would be two approaches you could use to map your data to the genome and generate transcript annotation that you could use for comparison to your current gene models. You can also examine the alignments to the genome to see how coverage corresponds to your transcript models.