About the CAGE data

[keliu.iluke]

Hi,everyone!
I am using ENCODE CAGE data in my analysis. However, I foud that the read length of the fastq file (which is downloaded from ENCODE,the cell line is H1-hESC) is 36, which is rather different from that of the CAGE tag they mentioned (27). Does anyone know why?

[davetang]

Hello,

the first three bases are the barcode sequence, and the next 6 bases (CAGCAG) is the restriction site for EcoP15I, which is used in the CAGE protocol to cleave 27 nt upstream of the site. So 36 - 9 = 27.

Have a look here for more information http://fantom.gsc.riken.jp/protocols/basic.html

Cheers,

Dave