View source for Wiggle BED to variableStep format conversion

The '''BED''' [http://genome.ucsc.edu/goldenPath/help/wiggle.html wiggle input format] is the most inefficient input format for wiggle tracks.  For each definition line the number of data points created is <em>chromEnd-chromStart</em> which can add up rapidly to the 300,000,000 data point input limit to wiggle custom tracks.

Please note the addition of the new (August 2008) [http://genome.ucsc.edu/goldenPath/help/bedgraph.html bedGraph] format to assist in overcoming this limit.

In many cases the '''variableStep''' and '''fixedStep''' formats are sufficient to display the same data that may have been encoded in the '''BED''' format.  If the '''BED''' formatted data has a consistent data item size, say for example 400 bases for each data line, it can be converted to a '''variableStep''' format with this simple script:

<pre>
#!/bin/sh

SPAN=400
S=inputFile.BED.format.txt
R=outputFile.variableStep.format.txt
rm -f ${R}
head -45 ${S} | egrep "^browser|^track" > ${R}
grep "^chr" ${S} | cut -f1 | sort -u > chr.list
cat chr.list | while read C
do
    echo "variableStep chrom=${C} span=${SPAN}" >> ${R}
    awk '{if (match($1,"^'"${C}"'$")) { print } }' ${S} | sort -k2n | awk '
{
    printf "%d\t%g\n", $2+1, $4
}
' >> ${R}
done
</pre>

A slightly modified version of this script [[Image:bedToWig.sh]] converts all bed files in the current directory.

This assumes there is a single track definition in this file: ''inputFile.BED.format.txt'' and the '''BED''' items were properly specified as [http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 zero-relative half-open] coordinates, where base position 1 of chr4 for example would be specified as: ''chr4 0 1''.  The coordinate system for '''variableStep''' and '''fixedStep''' input formats is ''one-relative'' coordinates where base position 1 of a chromosome is specified as 1.

This would convert a '''BED''' format line, for example:

<pre>
chr4  400  800 3.14159
</pre>

which occupies 400 data points in the internal representation of the wiggle data, to the '''variableStep''' format:

<pre>
variableStep chrom=chr4 span=400
401  3.14159
</pre>

which occupies a single data point in the internal representation of the wiggle data.


The use of the '''span''' specification in '''variableStep''' or '''fixedStep''' formats should be consistent for all data points.  It should be the same for all data points.  You do '''''not''''' want to mix different ''spans'' of data together in the same input submission.  The ''span'' specification in wiggle formats has a very specific use and is not to be used to specify arbitrarily sized data items (that's what the '''BED''' format is for).  See also: [http://genome-test.cse.ucsc.edu/~hiram/wigPresentation/slide160.html Pre-calculated Zoom (Span)] from [http://genome-test.cse.ucsc.edu/~hiram/wigglePresentation.html Wiggle Data Tracks].

See also:  [[Image:FixStepToBedGraph_pl.txt]] to convert fixedStep wigAscii to bedGraph.


[[Category:Technical FAQ]]