I was wondering whether it is possible to import alignment files from other aligners into quasR (e.g. STAR or Tophat2) in order, for instance, to run qCount on them.

Hi Sven

Yes, this is possible, as long as the alignemnts are stored as bam files. Have a look at the vignette (section 5.1
"Create a sample file"), where the three supported input files are described. In short: You create a sample file listing the bam files instead of the fasta/fastq files. Obviously, you will loose some functionality of QuasR.

Hope this helps, Hans-Rudolf