I have sent some samples the AGRF to be analysed by Human omni 2.5 .. However, I need to assess the CNV by using CNV partition plugins with genomestudio and I have some inquiry regarding the CNV detection parameter. Actually , I have designed my experiment to detect the genomic difference between the sample from patient diagnosed with cancer and his sequential samples after treatment .My concerns that I don’t have normal control sample from the patient and Its required that I get alteration related to the disease progression. In addition , I don’t have background in bioinformatics that enable me to get accurate analysis for my samples. I got some information from the genome studio manual that I have to create project , assess my data by CNV analysis function and visualize my data on Illumina genome viewer(IGV )and to exclude the normal CNV available in the CNV database. So , I need to get your advice about the CNV algorithm threshold and could you please help me to understand the important things that I have to consider when analyse my data.
abdo PhD Student