Bowtie and samtools - FASTA formatting and genomic coordinates

[kz26]

I'm in the process of aligning some RNA-Seq reads against a transcriptome. My transcriptome FASTA has headers in the following format:

>13405 chr4:34234-34507

As you might have guessed, the first part is a transcript ID. It seems that bowtie2 and samtools all use the transcript ID as the chromosome name and print out coordinate locations correspondingly. Is there any way to format the fasta files such that bowtie and/or samtools will use genomic coordinates instead? I could write a small program that converts the coordinates, but I'd like to know if there is an easier way.

[maubp]

This is a complicated problem if there is any splicing involved (introns to skip), or worse trans-splicing.

Since you apparently have chromosome sequences, why not just map to them directly as normal? That should make the downstream analysis much easier.