UR Fragmentation parameters

UR Fragmentation parameters

Joshua Dunn (guest) 05 Aug 2011 18:48

Hello,
Could you descibe the algorithm and/or equations you use to determine where breaks occur in UR fragmentation?

I'm interested in simulating a paired-end dataset, with uniform random fragmentation of transcribed cDNAs to an average size of about 200 nucleotides, and am wondering how to set the fragmentation parameters Delta and Eta to achieve this.

When you get a moment, please let me know!
Thanks,
Josh

Re: UR Fragmentation parameters

gmicha 10 Aug 2011 11:46

Hi Joshua,

we want to provide more information on the UR algorithm soon. You can control the average fragment size with Eta, set it to a value close to the average size you aim for. Delta controls the spread of the fragment size distribution, when deactivated (NaN) it is set dynamically for each transcript according to physical attributes.

Best,

micha