Entering edit mode
9.1 years ago
camilaubraz
▴
10
I have a file like this:
Index Name Chromosome Position GenTrain Score SNP ILMN Strand Customer Strand NormID
1 ARS-BFGL-BAC-10172 14 6371334 0.9014 [A/G] TOP TOP 2
2 ARS-BFGL-BAC-1020 14 7928189 0.9260 [T/C] BOT TOP 1
5 ARS-BFGL-BAC-10365 14 27005721 0.9176 [A/C] TOP BOT 2
7 ARS-BFGL-BAC-10793 14 29259114 0.9233 [C/G] TOP BOT 101
8 ARS-BFGL-BAC-10867 14 34639444 0.9293 [G/C] BOT BOT 102
The "TOP/BOT strand" file shows that if I have A/C or A/G (like index 1 and 5) is TOP, so the Allele A is A and the allele B is G or C. So, what is the strand that I should use? ILMN strand?
The file shows that if I have C/T or G/T is BOT, so the Allele A is T and Allele B is C or G. But in my file (index 2), the SNP is T/C BOT. what is the Allele A and B?
And index 7 and 8, what is the allele A and B?
Thank you!!