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What step size for wig files?
1
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2.5 years ago
YanO • 120
United Kingdom

Hi,

I am trying to convert bedGraph files to bigwig. I cannot use UCSC's bedGraphToBigWig script because later I need to convert to wig files using UCSC's bigWigToWig script, which just converts it back to bedGraph.

I have found an alternative script to do bedGraph to wig, but I need the step size, and don't know what it should be.

What default step size does UCSC's bedGraphToWig script use? (Is it 1?) How do I know which step size I should use? What step size do the wig files output from MACS have? (Is it 10?)

(I can't use 1 because I run out of memory when subsequently running wigToBigWig.)

Thank you!

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Sorry, I do not think I understand this. Could you clarify why can't you do bedGraphToBigWig -> bigWigToWig ? Why would it convert it back to bedGraph?

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I actually don't know why it converts it back into a bedGraph when bigWigToWig is used - it just does. See this answer from UCSC here: http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=5492&S=2925a24be1c20bb064fc09bd054f862d

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16 months ago
Canada

I had the similar problem a while ago: https://www.biostars.org/p/129830/#129855

The default step size is 1, and you can use the python script I wrote to convert bedGraph to wig:

https://github.com/mehrankr/slow_bedGraph_to_wig

You should run the script for each chromosome separately and them combine the outputs.

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