Goal

I am trying to get a distribution of Exons and intron sizes in Three-Spined Stickleback (Gasterosteus aculeatus).

Data downloaded

I downloaded some data from Ensembl. More precisely, I went there, selected "structure" in the "attributes" and selected

- Ensembl Gene ID
- Exon Chr Start (bp)
- Exon Chr End (bp)

Issues

There are two issues in these data:

1. Some exons end before they start
2. Some exons overlap

The first point is - I assumed - due to reversion during assembly, so I just reversed the start and end position when there was such inversion. The second point is more problematic as I don't know what such overlap could mean realistically.

Can you help finding the distribution of exon and intron sizes in three-spined stickleback?

Code

Preparation

# read data

d = read.table(file.choose(), header=TRUE)
names(d)= c("ID", "start", "end")

# Reverse exons when needed

toReverse = which(d$start > d$end)
s = d$start[toReverse]
d$start[toReverse] = d$end[toReverse]
d$end[toReverse] = s

Exon Sizes -> Looks good

# Exon sizes

ExonSizes = d$end - d$start
hist(ExonSizes) # Cool, looks good!

Introns Sizes -> Looks bad

# Intron sizes
# This is a little slow. One might have better to switch to C++.
# The idea is to look at the distance between the end of an exon and the start of the next exon within each gene.

d$ID = paste(d$ID)
IntronSizes = c()
uniquegenes = unique(d$ID)
nbgenes = length(uniquegenes)
i=0
exon = 0
for (gene in uniquegenes)
{
    i=i+1
    cat(paste0(i," / ",nbgenes,"\n"))

    while (TRUE)
    {
        exon=exon+1
        if (d$ID[exon] == gene) {
            IntronSizes = append(IntronSizes, d[exon+1,]$start - d[exon,]$end)
        } else 
        {
            break
        }
    }
}
hist(IntronSizes) # There are negative values. I don't know how to interpret them. 

hist(log(abs(IntronSizes))) # That looks good but I doubt it makes much sense!