[BioC] HT-Seq count and GTF

[Simon Anders]

Hi Jose

not sure what is going on.

The best might be to take one of these reads (find the read ID in IGV, 
then grep for it in the SAM file) and first check whether it might be 
multiply aligned ("NH" field). Then, make a mini SAM file with only this 
read and feed it to hseq-count, with the "--samout" option, to see what 
the script does with it.

   Simon