BigWigToWig produces ... bedGraph

[Charles Girardot]

Dear UCSC GB Team,

I am not sure this is the right place to post the question, so please forgive me if this is not.
I am trying to use a tool (CEAS) that requires a wig as input. Starting from a bigwig (actually downloaded from UCSC FTP, too big to use table export), I tried converting it to wig using BigWigToWig.

And discovered that the produced format is actually not wig but bedgraph :

> head crgMapabilityAlign50mer_filtered.wig
#bedGraph section chr1:3000000-3224494
chr1 3000000 3000059 1
chr1 3000078 3000339 1
chr1 3000340 3001992 1
chr1 3002016 3002213 1

I just tried downloading the latest binary and got the same result.
Is there some hidden option I should set to get proper wig format ?

Thanks for your help

Best regards

Charles


=====================================
Charles Girardot
Head of Genome Biology Computational Support (GBCS)
European Molecular Biology Laboratory
Tel: +49 6221 387 -8585
Fax: +49-(0)6221-387-8166
Email: charles....@embl.de
Web : http://gbcs.embl.de
Room V205
Meyerhofstraße 1,
69117 Heidelberg, Germany
=====================================

[Brian Lee]

Dear Charles,

Thank you for using the UCSC Genome Browser and your question about bedGraph in bigWigToWig output. 

Please see this recent conversation:https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/b0gzvACiug8/1n09CgGPu0MJ

The original data that is used to generate a bigWig can come from different formats. There is bedGraph, which is zero-relative, and wiggle, which is 1-relative.  In summary, if a bedGraph is used, the results from bigWigToWig will be bedGraph.

You mentioned that you are trying to use a tool (CEAS) that requires a wig as input. Since bedGraph input went into making this bigWig, the output from bigWigToWig will always be bedGraph, but you can use a script to change this bedGraph to a wiggle, see more here:http://genomewiki.ucsc.edu/index.php/Wiggle_BED_to_variableStep_format_conversion.

The wikisteps steps would convert a BED format line like chr4 399 800 3.14159 to wiggle data in the variableStep format:

variableStep chrom=chr4 span=400
400 3.14159

Our engineer shares a warning: Any bedGraph to wiggle conversion might produce a gigantic wiggle file. On the other hand, it might produce a much smaller file. It will depend upon how the bedGraph is structured. If the items are not the same sizes, or they vary in the gaps between the start positions, the conversion will blow up.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead togenom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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