Hi Anthony,
There are no known problems with the gene/codon BED tool, but if you
have an example of a problem, I will take a look.
Some items to double check first:
1 - Input is a BED 12 file
2 - Keep in mind that coordinates are "0-based, half-open start, fully
closed end" and always reported with respect to the forward strand.
Notation for bases 1-100 of a sequence would be written as: [0,100)
More details are at:
http://wiki.g2.bx.psu.edu/Learn/Datatypes#Bed
3 - This can make the math a bit tricky for transcripts aligning to the
negative strand. This wiki by Angie at UCSC is definitely the best at
explaining how to manipulate this type of data:
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
If you still think there is an issue, create a simple test of just a
single or few transcripts with the problems in a dataset, run the tool,
then tell me what you think is exactly wrong. Share the history using
"Options" (gear icon) -> Share or publish -> generate a share link,
copy, and send that back along with your comments to to my email address
directly (only). Simple is best, so that we can narrow down the exact issue.
For the aaChanges, this tool will work with most native Galaxy reference
genomes (the tool group name is confusing, sorry!). Just set the build
to be the same for all inputs. Stick with full builds (not variants -
e.g. use mm9, not mm9female). If you get an error about a missing build,
write back and I can let you know if the build is native or not, or
possibly even add it to the index if it was previously excluded for some
reason that no longer applies. Custom reference genomes are not
available for this tool, so if it does turn out that the public Galaxy
instance cannot make your particular build available, a local install
would be the alternative: http://getgalaxy.org
If you work out the gene/codon BED coordinates based on the additional
info, please reply to the list to let us know. If not, I'll just watch
for your shared link,
Best,
Jen
Galaxy team
On 7/11/12 2:07 PM, Antony Jose wrote:
Hi,
When using the gene BED to codon BED tool, I noticed that it is not
accurately reporting the codons that make up a gene. For example, some
of the codon are missing (particularly ones that span exon-exon
junctions. Also, when changing reading frame from one exon to the next,
the codons are not read appropriately and the reading frame appears to
be decided arbitrarily. Is this a serious known flaw with the tool or am
I missing something?
Also, is there a version of aaChanges tool that can be used with any
genome (not just human genome?).
Thank you.
Antony
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Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
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/
