[BioC] QuasR special case alignment

[Ugo Borello]

Good morning,

I am doing RNA-Seq analysis and I would like to perform an exploratory
analysis to first verify that 2 reporter genes are expressed in my samples.

Could the qAlign function perform an alignment of my short reads with two
reporter gene sequences, excluding the genome.
It seems, from my first attempt, that the 'genome' parameter is essential;
is this true?
Anyway how do I have to feed those sequences to qAlign and how do I have to
format my auxiliary file/files to see in the alignment statistics the number
of mapped reads for each reporter gene sequence separately?

Thank you in advance for your help.

Ugo

P.S. Let me say that QuasR is a fantastic package!