Help with getting data about the gene size distribution

Question

[ravi]

Hi,

I need to find the gene length distributions for multiple organisms. Can someone suggest me possible ways to get the information.

Ravi

[GouthamAtla]

Do you have annotations available for all the organisms of your interest ?

[Ashutosh Pandey]

You can directly query ucsc genome browser. I mentioned a mysql command in this post How To Get A List Of All Human Genes Above A Certain Length.

Answer 1

[Alex Reynolds]

Grab gene annotations for your organism of interest, and get them into BED format with convert2bed. For example, here are recent (GRCh38) human annotations via GENCODE:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_21/gencode.v21.annotation.gff3.gz \
    | gunzip --stdout - \
    | awk '$3 == "gene"' \
    | convert2bed -i gff - \
    > genes.bed

Then map genes against themselves to get their lengths. For instance, with bedmap:

$ bedmap --exact --bases genes.bed > gene_lengths.txt

Or with awk:

$ awk '{print $3-$2;}' genes.bed > gene_lengths.txt

The file gene_lengths.txt can be brought into R or similar to make a histogram:

$ R
...
> d <- read.table("gene_lengths.txt", col.names=c("lengths"))
> hist(d$lengths)