How To Convert Cel File To Wig File

Question

[Bingley]

Did anyone know how to convert chip-seq CEL files to Wig file format? Many thanks.

[Michael]

Do you mean ChIP-Chip, not chip-seq?

[Bingley]

Sorry, yes it's CHIP-chip data from Affymetrix Mouse Genome 430 2.0 Array. Any idea?

[seidel]

Are you sure you're doing ChIP chip on the Mouse Genome 430 2.0 array? This is not a tiling array, but rather is designed for 3' oriented gene expression measurements. You have a relatively small number of probes designed at various distances from the 3' ends of genes on the 430 2.0 array. I'm pretty imaginative, but it's hard for me to imagine what you'd be pulling down and measuring with such a non-uniform probe set.

Answer 1

[seidel]

The way I've done it, if you're talking about Affy Tiling arrays, is to use the Affy Tiling Array software (TAS), and then write a custom script to parse the result. The default options of TAS are to output binary files for reading in the Integrated Genome Browser (IGB from bioviz.org). However, there is an option to also spit out the results as text files. Those files are wig-like in that they have comment lines specifying the identity of a chromosome, and then subsequent lines in 'base value' format specifying the position and value measured at points along that chromosome which continue until a new chromosome identifier line is encountered. So it's fairly easy to write a script in perl or python to parse such a file and spit out wig output. The only catch is that on all the tiling arrays I've used (mouse, yeast, etc.) the first 5 chromosomes in the output file are numbered 1-5 (i.e. Chr1 through Chr5) but represent Arabidopsis control sequences (if I recall correctly). Thus the data for the organism of interest is found the second time Chr1 through Chr5 appear in the file.

I don't know of an option for going from CEL files to wig directly. TAS didn't do it as of 2010, but it may have been updated since then (I doubt it). There was some talk of getting TAS to run in linux (rather than Windows), I never got it to work. The Affy Powertools Forums on the Affy web site was a good source of information, if you can find them, and if they still exist.

Answer 2

[Bingley]

Thank you very much, Seidel. It's really helpful.