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!
1 answer
I had the similar problem a while ago: bigwig to wig conversion, getting bedgraph
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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written
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mehran.karimzade
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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?
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