Hello list, 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: #example BED-file: chr17 3763624 3794037 uc002fwt.2 0 - 3765504 3788981 0 16 1953,104,129,88,74,54,200,89,22,37,134,52,54,48,403,51, 0,5577,9156,9470,12223,13078,15892,20015,21296,22197,22711,23098,23553,24049 ,24997,30362, #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? Thank you. Regards Chris
Hello Chris, Thank you for reporting the problem, it was indeed a calculation error with the BED-to-Codon operation. The code has been corrected, but has not been placed onto the Galaxy main server yet. Look for it in the next week and please let us know if you have more comments. Thanks again! Best, Jen Galaxy team On 3/22/11 4:52 AM, Christopher Schroeder wrote:
Hello list,
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:
#example BED-file:
chr17 3763624 3794037 uc002fwt.2 0 - 3765504 3788981 0 16 1953,104,129,88,74,54,200,89,22,37,134,52,54,48,403,51, 0,5577,9156,9470,12223,13078,15892,20015,21296,22197,22711,23098,23553,24049,24997,30362,
#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?
Thank you.
Regards
Chris
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
participants (2)
-
Christopher Schroeder -
Jennifer Jackson