dimension of read and exon dimension

[Mp]

I have one sample with  1x50bp. I use star for alignment but unfortunately all the exon less tha 50 bp I was not able to align.
Have you any explanation on this? How can I resolve?

[Alexander Dobin]

Hi Maurizio,

could you please give me some specific examples, I am not sure I understand what the problem is.

Looking at the alignment signal on the browse is probably the best way.

Cheers

Alex