what are the concerns when read length is longer than the reference ?

[mallela]

Hi,

I'm dealing with the expression data of shRNA where the reference sequence (antisense sequence) is about 22bp and the length of the reads produced by ion proton average at 125bp. This is the case where the reference sequence length is smaller than the read length. I am using bowtie for alignment with 0 mis-match stringency. Are there any concerns ?

Please bear with me if this is a naive question.

Thanks!