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bedgraph to bigwig

Hi,

I am analyzing Nanopore methylation data and I would like to use plotHeatmap from deeptool. The result of the methylation call I have is a bedgraph with the position of the modification and in the 4th column a value between 0 and 1, where 1 means 100% of the reads at that position present the methylation signal.

I am using bedGraphToBigWig or wigToBigWig to convert bedgraph to bigwig

bedGraphToBigWig in.gedgraph genome.size out.bw
wigToBigWig in.bedgraph genome.size out.bw

The problem is that in the output (bigwig file) de values range from 0 to 0.2 instead of 0 to 1

Is there another way to plot the data or obtain the bigwig file with the real range? The y-axis is not representing the real data (none of the values in bigwig are 1).

Thank you in advance.

Florencia

bigwig bedgraph deeptools methylation
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updated by Ram Ram • written by Florencia • Florencia

Neither of these tools alter the score column. It must be a problem with the bedGraph, please confirm the data range in it is actually correct.

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written by ATpoint ATpoint

Thanks for your response. You were rigth bedGraphToBigWig is working well. I looked the data on IGV choosing auto scale so that the max height is set to the highest point in the signal and the values range from 0 to 1. The problem now is how to set that on deeptools. Do you have any idea? Thanks again.

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written by Florencia • Florencia

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