Definitions from 'summary' tool

[raflynn]

Hi All,

[raflynn]

I had three issues/questions that arose after I was able to run the iCount summary tool.

1. When using the 'summary function, there are terms like "sites" and "events" -- what the difference is between these two?

2. When using the 'summary function, the 8 categories that come out are CDS, 3UTR, 5UTR, gene, intergenic, intron, ncRNA, and transcript; which together sum to 1. I am confused about the definitions of gene vs transcript vs CDS... What the differences between these types // is there a place where these definitions are coming from?

3. Is it possible to extract hits (mRNA targets) based off their annotation in the summery.tab file? For example, if I wanted any mRNA that had RT stops as annotated in the summary.tab file, is it possible to retrieve those gene-ID's?
   Thanks!
   Ryan