intronic reads and unspliced reads differences
Intronic reads and unspliced reads are two different types of RNA sequencing (RNA-seq) reads that can be generated from the same transcript.
Intronic reads are reads that map entirely within an intron of a spliced transcript. These reads represent transcripts that have not yet been spliced, and therefore have not yet had their introns removed. Intronic reads can be generated from a variety of sources, including unspliced or partially spliced pre-mRNA, as well as nascent transcripts that are still being actively transcribed.
Unspliced reads, on the other hand, are reads that span a splice junction and therefore cover both exonic and intronic regions of a transcript. These reads represent transcripts that have not yet been fully spliced, and may include reads from partially spliced pre-mRNA, as well as nascent transcripts that are still being actively transcribed.
The main difference between intronic and unspliced reads is that intronic reads map entirely within an intron, whereas unspliced reads span a splice junction and cover both exonic and intronic regions. Therefore, intronic reads can only be generated from unspliced transcripts, whereas unspliced reads can be generated from both spliced and unspliced transcripts.
Intronic reads and unspliced reads can provide different types of information in RNA-seq data analysis. Intronic reads can be used to detect unspliced pre-mRNA and other nascent transcripts, which can be informative for studying transcriptional regulation and splicing dynamics. Unspliced reads can be used to identify alternative splicing events and quantify the expression levels of different transcript isoforms.