This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How big is the human exome?

Dear All

According to your experience how big is the size of the human exome in megabases?

Mining the web there are tons of sites that report roughly 30 Mb but all of them are dated on 2010-2013 and I suspect this overwhelming information is related to an extensive cut and paste of old statistics of the human genome

Moreover the kits for exome capture from Agilent (Agilent SureSelect All Exon V6) now target 60 Megabases.

What do you think about this?

Thank you

Guido

exome capture
• 5,574 views • link
written by guido.leoni • guido.leoni

Exome capture kits also include UTR and miRNA content etc - therefore targetting more than 30 Mb.

• 0 views • link
written by WouterDeCoster WouterDeCoster

According to the agilent web site the kit that comprehends also the UTR regions covers 91 Mb

• 0 views • link
written by guido.leoni • guido.leoni

2 answers

Calculate it yourself, see here in a previous post how to do it with a gtf file (which you can download from ensembl).

• 0 views • link
written by Benn Benn

Just to add a piece of information I downloaded the gtf file from Ensembl and ran the following command

awk '(($3=="exon") && ($0 ~ / gene_biotype "protein_coding"/)){print $0}' Homo_sapiens.GRCh38.95.gtf | gtf2bed - | bedops -m - | awk 'BEGIN{FS="\t";count=0}{count=count + ($3-$2)}END{print count}'

The estimated size for the exome in protein coding genes is around 99Mb (99.810084)

• 0 views • link
updated by Benn Benn • written by guido.leoni • guido.leoni

Log in to answer this question.

More posts like this