Conversion Of Bar To Wig Format

Question

[Ian]

I use a program called MAT for peak calling in ChIP-chip experiments. It produces a binary output (BAR) file for viewing the probe intensities. This file (as far a I know) can only be viewed in the IGB viewer, but I would like to be able to view the data in the UCSC browser in the form of a WIG file.

There is a tool (available from the MAT authors Google group 'MAT.announce') called Bar2Wig.py, but the output is not compatible with UCSC browser.

Has anyone managed to successfully convert BAR to WIG?

Thank you!

[Istvan Albert]

Could you specify in what way is the output not compatible with UCSC? since the wiggle format is so simple it could just be some small issue that needs to be dealt with

Answer 1

[Istvan Albert]

A few years ago I have created a simple script that converted bar files to wiggle format.

You can find it here,

Alas I have not used it recently (within a year or so) thus if the MAT internals have changed then this tool will not work properly anymore.

[Ian]

That's great - just what i wanted!

[Pierre Lindenbaum]

now you can validate Istvan's answer...

Answer 2

[Michael]

I don't know this tool, but the UCSC genome browser also loads bed files. According the tool page:

MAT returns two types output files: the .bar files which contain the MAT score for each probe which can be imported to Affymetrix Integrated Genome Browser (IGB) for visualization; a .bed file with the chromosomal coordinates of all the ChIP-regions with MAT score and repeat (including segmental duplications) flag which can be loaded into UCSC Genome Browser.

[Ian]

Unfortunately the BED file only shows the binding regions and not the intensity of binding. But thanks nonetheless.

[Michael]

I misunderstood. Indeed you want to view the probe intensities in UCSC.