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