I already analysed some of our data with your framework and I want to thank
you for your great work. But lately I stumbled on some strange behavior - I
used the "aaChanges"-tool, as well as the Gene "BED-to-Codon"-tool with the
same Gene-BED-File and compared the results. What I did:
chr17 3763624 3794037 uc002fwt.2 0 - 3765504 3788981 0
#example-output of "aaChanges"
chr17 3775847 3775848 C uc002fwt.2 Glu:Gly 375 T
#example-output of "BED-to-Codon"
chr17 3773172 3773175 uc002fwt.2 0 -
chr17 3773175 3773178 uc002fwt.2 0 -
chr17 3773178 3773181 uc002fwt.2 0 -
chr17 3775849 3775852 uc002fwt.2 0 -
chr17 3775852 3775855 uc002fwt.2 0 -
Comparing both results, the "BED-to-Codon" actually presents no codon at
position 3775848 - here the fist codon is starting at 3775849. But in fact,
looking at the ucsc browser, "aaChanges" is right. There are another few
examples (~5/1500 snps) and apparently most of them are positions among the
first codon in an exon.
Did anyone meet this problem before? What is my mistake?
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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: