[Genome] liftover and wiggle

[Amanda Miotto]

Is it possible to liftover wiggle files that are in the fixedstep format,
or will I need to include a startbp and stopbp and chr for all scores?



Amanda Miotto
a.mi...@griffith.edu.au

Software Engineer.
Research Computing Services
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Griffith University, NATHAN 4111, AUSTRALIA
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[Brooke Rhead]

Hello Amanda,

There is currently no option for the liftOver utility for using wiggle
fixtedStep format. You will need to convert your data to one of the
formats, such as BED. You can see the accepted format options for
liftOver by typing the command with no arguments at the command line.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

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[Brooke Rhead]

Hello again Amanda,

One of our developers has pointed out that we have some scripts in the
genomewiki for converting between wiggle and BedGraph formats:

http://genomewiki.ucsc.edu/images/9/9d/FixStepToBedGraph_pl.txt
http://genomewiki.ucsc.edu/index.php/Wiggle_BED_to_variableStep_format_conversion

BedGraph format is described here:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html
Data in this format can be used with the liftOver tool as if it were
regular BED data. The main difference between the formats is that the
column that normally contains a name in BED format (column 4) contains a
data value in BedGraph format.

I hope this is helpful.

--
Brooke Rhead
UCSC Genome Bioinformatics Group