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
The information transmitted is intended only for the person or
entity to which it is addressed and may contain confidential
and/or privileged material. Any review, transmission,
re-transmission, dissemination or other use of, or taking of any
action in reliance upon this information by persons or entities
other than the intended recipient is prohibited. If you received
this in error, please contact the sender and delete the material
from any computer.
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org