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# System prepended metadata

title: '**Intron retention detection and quantification from full-length bulk RNA-seq**'

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# **Intron retention detection and quantification from full-length bulk RNA-seq** 

**What the project is about?**
In an RNA-seq sample, determine which transcripts are retaining introns, and what are the abundance / retention levels of those introns. These introns can be anywhere on the transcript, and may often be evidence of splicing errors (associated with e.g. disease)

**Characteristics of the data:**
full-length, bulk RNA-seq data
short paired end (or single end) reads

**Main goals:**
Coming up with a nice probabilistic model like the one for normal quantification
Computing the PSI value for each intron (or something like that)

**Possible approach:**
* Finding the potential retained introns:
Start by aligning all the reads to genome+transcriptome simultaneously, then looking at all the alignments, for example there are some of the reads that only map to genomic regions, and it doesn't mean that they align best to the genomic regions, they **only** align to the genomic regions. (Ofcourse with the default alignment threshold which is 0.65)
Using the the signal from the above observation, maybe with some modification, the set of candidate introns might be selected.

* Computing the expression ratio for the introns:
First of all, just quantify all the transcripts using all the alignments from the reads to transcriptome.
Then, use the counts of transcripts spanning each intron as some kind of prior for an intron to be retained. After that, do a new round of quantification only for the intron sequences using the priors we just calculated. If there are multiple isoforms spanning an intron, we could try computing the prior by averaging over their expression value.

* The probabilistic model for expressing the introns

Suppose there are $n$ introns in a gene with $m$ isoforms, then, we can introduce (and later estimate) the following probabilities in the main quantification model:
>$P(i,j) =$ The probability of retaining intron j in transcript i
>$P_{noIntron}(txp_i) = 1-\sum_{j=1}^{n} P(txp_i,j)$ : The probability that no intron is retained in transcript i


By assuming the independance between the intron being retained in each trnascript, the probability of retaining an intron can be calculated by marginalizig over all the transcripts in each gene. so:
>$P_{retain}(int_j) = \sum_{i=1}^{m} P(i,int_j)$