I want to use an online software, CTLPScanner. It requires array segment file in text file format. I would really appreciate if anybody can teach me on how to convert the .cn file to .txt file. Thank you.
Which program did you get the .cn file from? Its not a well known file format.
If you like, you can send me a sample and I can check whether it can be converted. Pls make sure there's no confidential data in it.
Inham Hassen I am using SNP 6.0 array from Affymetrix. After scanning, I got the CEL files. Then I used the Genotyping Console software to create copy number and segment files.
Most of these words are beyond my comprehension. However, I did a bit of googling on the output file format of Affymetrix and I noted that the site says:
"The format of the CEL file is an ASCII text file similar to the Windows INI format ", so technically, it should be as simple as copying the data to notepad and saving them as .txt file.
It may be possible that the Affymetrix output is in ASCII character set (which is a very old format) and the CTLPScanner (which is a web service) does not detect ASCII. A wild guess but it may happen.
Is there any possibility of sharing a sample (even if there's one line of data, it should be enough). 1. I may need a sample of the output file (that you got from Genotyping console) and 2. the type of file that CTLPScanner needs.
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