Question: Explore CNV data from illumina Array
0
gravatar for melania 2282
6 weeks ago by
melania 2282100
melania 2282100 wrote:

Hello, I have received out put from OncoArray illumina array of CNV data.
The file is a .txt like this :

Sample_ID     Sample_1           Sample_2              Sample_3
variant_1   logR AlleleB X Y    logR AlleleB X Y    logR AlleleB X Y
variant_2   logR AlleleB X Y    logR AlleleB X Y    logR AlleleB X Y
variant_2   logR AlleleB X Y    logR AlleleB X Y    logR AlleleB X Y

Each sample has one column, inside this colum 4 values are space separeted.
I would like to know if there is any CNV exploring program (Like PennCNV) that could accept this file as input ? I already extracted the B allele and log R separatly for all sample but I would like to explore the results more with specialised programs especially visually ... Do you have any suggestion ?

Thank you very much

cnv snp illumina • 117 views
ADD COMMENTlink modified 6 weeks ago by bernatgel2.8k • written 6 weeks ago by melania 2282100
1
gravatar for bernatgel
6 weeks ago by
bernatgel2.8k
Barcelona, Spain
bernatgel2.8k wrote:

If you have a file for each sample, you can use the R/Bioconductor package CopyNumberPlots to create plots of your raw data and if you call copy number variants (with PennCNV or any other) you can also plot the calls along your data.

ADD COMMENTlink written 6 weeks ago by bernatgel2.8k

Thank you, but PennCNV have a very special input, do you know any other program that i can test it ? thanks

ADD REPLYlink written 6 weeks ago by melania 2282100
1

If it's cancer samples, you can try with ASCAT, if it's germline data, then maybe DNAcopy or GenoCN?

ADD REPLYlink written 6 weeks ago by bernatgel2.8k
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