bigwig file to bed graph

Question

[rajesh]

Hello everyone I have downloaded bigwig file for GM12878 H3K27Ac Mark (Often Found Near Regulatory Elements) on GM12878 Cells from ENCODE.

This contain the data for acetylation, which marks for transcriptinally active region. When i convert the bigwig file to bedgraph, there comes a datavalue at fouth column.

#bedGraph section chr1:10075-56525
chr1    10075   10100   0.92
chr1    10100   10125   1
chr1    10125   10150   1
chr1    10150   10175   1
chr1    10175   10200   2
chr1    10200   10225   2
chr1    10225   10250   2

What this data value signifies. Is it for acetylation marks. How to know the coordinates for the acetylation peaks.

thanks in advance

[ATpoint]

Please use the formatting bar to indicate code and example data for improved readability. I've done the changes for you this time.

[rajesh]

thanks.. alot for this

[Vitis]

I'm not familiar with H3K27Ac Mark data, but both BigWig (condensed version of wig and bedGraph) and bedGraph should have the fourth column indicating some kind of values at the genomic location or region. This could be sequencing coverage, expression level or methylation mark. So having the fourth column would not be a surprise. I think you need to dig into how the data was generated to find out the meaning of the value.

Answer 1

[ATpoint]

Column 4 can be any score of choice that can be associated with the interval defined by col1-3. Can be an enrichment of ChIP over input, mean CpG methylation level, read count per million, the GC content etc. In case of H3K27ac, it is probably an enrichment over input or the read count but you'll need to check if the download portal provides this information. Check the main ENCODE data portal for H3K27ac data, they have plenty of it and better documentation than the link you shared.