How To Know Which Reads Is In Intron Or Exon

Question

[Sara]

Hi everyone,

I mapped the short read sequence of miRNA with an species different from human and mouse. The genome is completed in this species. How I can know if these reads are in intron or exon?

Cheers,

sara

Answer 1

[Jeremy Leipzig]

• Snps Location Annotations
• Basic Bam File Annotation
• http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-RNA-Seq-Analysis

Answer 2

[Larry_Parnell]

Every microRNA (miR) gene that I have seen mapped to the genome - in mouse or human (or other species) - maps either within an intron of a protein-coding gene or as a distinct transcription unit outside of any other gene. Thus, I would not expect to find any miRs mapping to exons.

The question is a bit unclear to me, so I am guessing here. If you have sequence reads and need to map these as within exons, then they should map to the RefSeq mRNAs. Also, see Jeremy's response.