Overlapping regions in bedGraph

Question

[Aayush]

I tried to convert my bedGraph file to bigwig file using "bedGraphToBigWig" tool. while doing so, I ran this code :

> bedGraphToBigWig H3K4me3.unique.bedGraph hg38.chrom.sizes H3K4me3.bw

But I received this error :

Error - overlapping regions in bedGraph line 280 of H3K4me3.unique.bedGraph

How to solve it ?

[cmdcolin]

I would consider trying to find out why this occurred in the first place, as this is somewhat unusual.

[Ram]

Adding to this, was the bedGraph created manually or is it the direct output of a different tool?

[Aayush]

I created it manually.

Actually, I had a .bedGraph file

"GSM1204470_MDAMB231.H3K4me1_1.hg19.tags.bedGraph" which has hg19 as reference genome.

But then I used "liftOver" tool and changed it to hg38 reference genome and saved the output as .bed file.

Then, I converted .bed file to .bedGraph by manually adding "score" column.

Thus prepared .bedGraph file is now being converted to bigwig file and this issue is shown.

[Ram]

Sort the liftOver file and check for overlaps. lifeOver can be imprecise.

[ATpoint]

Seconding the others, this should not happen, so it's an error in the upstream generation. Common tools that do bedGraphs properly:

• deeptools bamCoverage
• bedtools genomecov
• inside R: rtracklayer::export() where input could be a GRanges object.

It might be as simple as a 0-based vs 1-based problem here, so please address question from @cmdcolin