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.
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).
On 12/11/13 12:14 PM, Tomaszewicz, Keith wrote:
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.?
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
. 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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at: