Is there an automatic way to search transcripts that align with intergenic sequences in a genome?

Question

[albersnz96]

I have a problem with the IGV program. I am comparing the information of all the annotated genes for a yeast (.gtf file) and the mapped RNA-seq reads with its genome performed with Tophat (the genome is a .fa file and the mapped sequences is a .bam file). I am looking for transcripts that align with intergenic sequences to correct the annotations in the .gtf file; therefore, I would like to check the number and localization of each transcript that align with an intergenic sequence. Could somebody tell me if there is a way of doing this analysis in an automatic form using IGV or if I need the use of another Bioinformatics tool?. Thank you for your help.

[PoGibas]

Try bedtools intersect (what you want is to extract regions with reads that doesn't intersect annotated genes).