Hello folks

I'm new to the RNAseq field and I was wondering if I could have some advice?

I want to identify transcription start sites from my RNAseq. So far, I have trimmed and aligned by reads to my reference genome using bowtie2. I took the output BAM file from bowtie and used that in cufflinks. However, cufflinks seems to be ignoring large regions of my genome which have a massive abundance of aligned reads. Please could you advise me on how to address this or perhaps an alternative path to identifying start sites.

Thanks
David