Wiggle File 2 Bed File

Question

[Varun Gupta]

Hi I have a wig file(variable step) I want to convert this wig file to a bed file. Can anyone tell me how to do that.

Thanks in advance

Regards Varun

Answer 1

[Pierre Lindenbaum]

googling for wig2bed returns a python script : http://code.google.com/p/chip-seq/source/browse/formatconvert/wig2bed.py ( http://code.google.com/p/bedops/wiki/wig2bed )

[brentp]

You mean: http://code.google.com/p/chip-seq/source/browse/branches/formatconvert/wig2bed.py? That's fixedStep. Though the latter tool you mention seems to support variable step.

Answer 2

[Alex Reynolds]

The wig2bed application that is part of the BEDOPS suite will convert both variable- and fixed-step WIG inputs to UCSC BED output.

Answer 3

[Damian Kao]

Here is a perl script to convert wig to a bedgraph format: http://genomewiki.ucsc.edu/images/9/9d/FixStepToBedGraph_pl.txt