Filtering out transcriptome data

[Ahaswer]

Hi,
I have RNA-Seq reads of mutant plant which has few insertions (unknown sequence) in comparison to wild reference genome. I want to filter out all reads which are the same as in reference so I can get only those insertion sequences. Should I map my reads straight to reference to filter it out or try to do de novo assembly and then map contigs to reference genome? What do you suggest?

[cascoamarillo]

A quick solution would be to use bowtie with the option --un; which writes unmapped reads to a file and then work with that.

[Ahaswer]

Thanks cascoamarillo, I will proceed as you suggested. But using bowtie2 will remove also reads which are located at exons boundaries so that I will get those files in unmapped reads, am I correct?