What step size for wig files?

Question

[YanO]

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!

[Saulius Lukauskas]

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?

[YanO]

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

Answer 1

[mehran.karimzade]

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.