using STAR to confirm crispr KO?

[Saskia]

Hi,
is it possible to set the STAR parameters so that I can check if a gene as been "deleted" by CRISPR KO in RNA-seq data?
I played around with an example file where FOXO1 has been deleted using CRISPR KO, and I still get counts for the gene but when I look at the alignment it looks like it is deleted in the sense that there are only small alignments at the start and end of the the gene sequence. See fig here:

But the count for that gene us still around 1200.

What would be a good parameter so set to say "count as 0 if only 1% of the DNA of a gene has been covered" or "count as 0 if the insert is 100K bp". Or am I looking at this the wrong way all together?

many thanks
satz