Hello Asuncion,
FlyBase genes can be imported to Galaxy using "Get Data -> UCSC Main
table browser". To join in the annotation with your data, use BED format
with the "Operate on Genomic Intervals" tools or use GTF with the "NGS:
RNA Analysis" tools. Please note that the data from UCSC is not from the
most current FlyBase release. Here is a history where I imported the
data as an example and annotated the date:
http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/dm3-flybase-genes
Another choice is to obtain the most current release of Flybase directly
from the source at:
ftp://ftp.flybase.net/releases/FB2011_01/dmel_r5.33/gff/
Please note that the release data at Flybase will require a bit of
tuning before use. The general path would be to ftp the data locally,
modify the files, then upload into Galaxy. Specifically, you will want
to adjust the chromosome names to be in the exact format as in Galaxy's
native dm3 assembly (see the chromInfo file, dataset #3 in the shared
history above). Some filtering of the release will also be necessary to
limit the content to gene annotations only (if desired). And as the
files are in GFF format (specifically GFF3), not GTF, that will need to
be adjusted as well, unless you want to use BED format. If BED format is
the goal, then you can just "Get Data -> FTP" the GFF data into Galaxy
and using the tool "Convert Formats -> GFF-to-BED" should be possible.
Best wishes with your research and please let us know if we can help again,
Jen
Galaxy team
On 1/25/11 1:35 AM, Asuncion Lago wrote:
Hi,
I have used the RNAseq tools to calculate the FPKMs values, now I would like
to know how I can link this values with the gene name or the Flybase ID in
my particular case. I have been trying in different ways without success.
Could you help me, please?
A
El 17/12/10 16:57, "galaxy-user-boun...@lists.bx.psu.edu"
<galaxy-user-boun...@lists.bx.psu.edu> escribió:
Your mail to 'galaxy-user' with the subject
Upload problem
Is being held until the list moderator can review it for approval.
The reason it is being held:
Post by non-member to a members-only list
Either the message will get posted to the list, or you will receive
notification of the moderator's decision. If you would like to cancel
this posting, please visit the following URL:
http://lists.bx.psu.edu/confirm/galaxy-user/6682d97aabcbfc0d3b720c1e020e8c644d
76e27d
------ Fin del mensaje reenviado
_______________________________________________
galaxy-user mailing list
galaxy-user@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-user
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
_______________________________________________
galaxy-user mailing list
galaxy-user@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-user
