Entering edit mode
6.5 years ago
Myosotis1979
▴
30
Dear all I have generated a gvar file using Canary algorithm to call copy number polymorphisms. Then, I generated a summary file of it using PLINK. Here a subset of the file:
NAME FIELD VALUE
CNP3 CHR 1
CNP3 BP 777800
CNP3 CNV no
CNP3 ALLELIC no
CNP3 GCOUNT 42
CNP3 INTEGER Y
CNP3 A 1
CNP3 [2] 1
CNP3 0/0 59:0
CNP3 AA/null 42:0
CNP4 CHR 1
CNP4 BP 1640120
CNP4 CNV yes
CNP4 ALLELIC no
CNP4 GCOUNT 43
CNP4 INTEGER Y
CNP4 A 1
CNP4 [1] 0.02326
CNP4 [2] 0.9767
CNP4 0/0 58:0
CNP4 A/null 1:0
CNP4 AA/null 42:0
CNP6 CHR 1
CNP6 BP 8108521
CNP6 CNV no
CNP6 ALLELIC no
CNP6 GCOUNT 41
CNP6 INTEGER Y
CNP6 A 1
CNP6 [2] 1
CNP6 0/0 60:0
CNP6 AA/null 41:0
I have many questions: - How to distinguish which are polymorphic CP ? - How to convert this file into an input file to STRUCTURE (population stratification software) as well as for the PCA analysis? - Should I use all these CNP for linkage desequilibrium analysis or should I filter to those which have "yes" value in this file ? Your help is valuable as I spent a lot of time searching for a tutorial in vain. Many thanks
Hello, in which format was your original ata? - CEL files? Which platfom? - Affymetrix SNP 6.0?
Hello, CEL files for Affymetrix 6.0 plateforme
okay, and how did you perform Canary? - using Affymetrix Genotyping Console?
I performed Canary according to the BirdSuite pipeline
...and what is the input format required for STRUCTURE? You know that you can do PCA and MDS in PLINK, too?
You already have your data in PLINK PED or BED format, right?