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Old 02-19-2010, 08:31 AM   #1
anna_vt
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Default wig file compression

Hi,

I have written a script to produce wig files from Eland aligned output, however the files are mostly too large to load onto UCSC for viewing (despite being split by chromosome and gzipped).

I would like to decrease the resolution of the files by having larger a larger step size than 1base, but have been unable to find any documentation on how you would do this. Would taking the average base height across a step be a suitable method or is there another way this is done?

Many Thanks for any help,
Anna
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Old 02-19-2010, 08:36 AM   #2
Thomas Doktor
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You should try converting your wig files to the bigwig format as described here: http://genome.ucsc.edu/goldenPath/help/bigWig.html

You do need to be able to store your files on a web-accesible server.
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Old 02-19-2010, 12:28 PM   #3
dawe
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Quote:
Originally Posted by anna_vt View Post
Hi,
I would like to decrease the resolution of the files by having larger a larger step size than 1base, but have been unable to find any documentation on how you would do this. Would taking the average base height across a step be a suitable method or is there another way this is done?

Many Thanks for any help,
Anna
Besides the bigWig format (which you should definitely look), there's also the bedgraph format which is still in text file but allows you to give a value for a specific span which can vary in size. regions without any reads are excluded.
About the function... it depends on the span you are using, the size of your features and which detail you want to keep... popular functions are average, median and maximum in a defined span (10 bp to start)...
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