Hi Keith,

The first protocol in this paper does a very similar task. Just maybe skip the parts where you do the counts, instead use the merged file. If you note, the "name" of the exons includes the transcript, the coordinates, and the exon's position in the transcript.
https://usegalaxy.org/u/galaxyproject/p/using-galaxy-2012

The second protocol in the above has some examples of manipulating a file that is seemingly very far from interval/bed format into one that is (see the last part of that section).

If you need to map to the gene name, then that can also be extracted from the UCSC table browser and then joined in with the data, using the transcript names as a common field. There is a user guide for the Table browser linked under the form (scroll down).

Good luck!

Jen
Galaxy team


On 12/11/13 12:14 PM, Tomaszewicz, Keith wrote:
Hi,
I am new to galaxy but I think your tools may be what I need. I simply have a .bed file with amplicons and their chromosome, start and stop location in the human genome. I simply want to align the .bed file amplicons to the HG19 and have a file I can export that which will tell me what exons are covered by the amplicons. Is this possible? If so I have no idea how to do this yet using galaxy. Do I need to upload the HG19 or is that in your system already. Can codons that are covered by the start and stop locations be extracted as well.?
Thanks
keith
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