Identifying introns

Question

[bioinformatics.queries]

Hello everyone

I have very basic question. I have RNA sequencing data and I would like to identify the intronic sequences. Does the RNA-seq data have both introns and exons? When I googled, it says that RNA-seq data has exon-exon binding. My question is how to obtain the intronic sequences from RNA-sequencing data ?

Thanks

Answer 1

[Friederike]

Does the RNA-seq data have both introns and exons?

That depends on the type of RNA-seq library preparation that was done. Some prep kits exclude immature RNA (which would contain introns), other kits do not. This paper by the Griffith brothers has some good explanations on the different types of RNA-seq data that can be generated, specifically this image might be helpful for your question at hand.

how to obtain the intronic sequences from RNA-sequencing data ?

As the other answer indicates, you simply have to align the reads to the full genome which will include intronic, exonic and non-genic regions. If your data contains intronic sequences, those will align to the annotated introns.

[bioinformatics.queries]

Thank you so much for your response.

Answer 2

[Zhilong Jia]

mapping the reads to reference genome with annotation, which includes the intron locations in the genome.

[bioinformatics.queries]

Thank you so much for your response

[Ram]

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