Extracting FASTA Sequence by Transcriptomic Coordinates

Question

[eyal.peer]

I'm aligning RNA-Seq data using STAR and I'm choosing two outputs - genomic and transcriptomic.

I want to use the transcriptomic coordinates for peak-calling, thus getting a bed file of peaks.

The peaks then will be in transcriptomic coordinates and not genomic.

Is there an existing tool to extract FASTA sequence based on transcriptomic (GENCODE V19) coordinates?

If not, how about a tool to quickly convert transcriptomic coordinates to genomic and vice versa?

[Devon Ryan]

If you want things in genomic coordinates, then why not just align to the genome?