Question

How to convert bedgraph to wig

0

Entering edit mode

ferbecneu • 0

@ferbecneu-16188

Last seen 5.1 years ago

Hi, i would like to convert a bedgraph document to wig format for downstream data analyisis for which I require a wig file.

I have it in the format:

track name=CD6_1_RPMs description="read per million" type=bedGraph

chr1 3005880 3006265 0.788085378200589

chr1 3006269 3014101 0.788085378200589

Its from a 4c-seq RPM normalized counts and the coordinates represent fragments generated from RE digestion.

Is it possible to do this with Bioconductor?

Thank you very much!

rtracklayer genomicranges • 3.6k views

ADD COMMENT • link updated 6.9 years ago by Michael Lawrence ★ 11k • written 6.9 years ago by ferbecneu • 0

score 1 · Answer 1 · 2018-11-26

1

Entering edit mode

Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.9 years ago

United States

bedGraph used to be a variant of WIG, so it might work as-is. But if not, then the ranges all need to be the same width, so in general they will all need to be length one. The GPos object is an efficient way to represent that, so you could load the data, convert to a GPos, and export.

Something like:

library(rtracklayer)
bg <- import("foo.bedGraph")
gp <- GPos(bg) # unfortunately need to carry over metadata manually
score(gp) <- rep(score(bg), width(bg))
export(gp, "foo.wig")