Greetings!
Debugging my script I found the following annotation, and I think there is a
problem:
C.elegans, assembly ce6, CHR
refGene table entry:
#bin name chrom strand txStart txEnd cdsStart cdsEnd
exonCount exonStarts exonEnds score name2 cdsStartStat
cdsEndStat exonFrames
596 NM_061576 chrII + 1467732 1469600 1467752 1469560 7
1467732,1468089,1468422,1468750,1468880,1468999,1469128,
1468040,1468373,1468542,1468830,1468953,1469069,1469600,
Through genome browser the first codon starts at position 1467752 and not
at 1467732 (as in database). If I use the data from database, it is
impossible to get the right protein sequence.
Is there any possibility to handle such cases automatically (I mean by some
script and not by looking at the result)? Actually, I find this one by
accident :)
Sincerely Yours,
Alexandra Rapoport
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