How to convert BED file of ATAC seq to Bigwig file

Question

[kuangliang128]

I want to convert such kind of BED file into Bigwig file for visualization on UCSC, and I have tried the "rtracklayer", the error message is as follows:

> library(rtracklayer) #bioconductor
> 
> bed_loaded <- import(con="~/R/GSM3733316_E59_distal_femur_peaks_hg19.bed.gz", format="bed") #no need to unzip .gz
> # bed_loaded <- import.bed(con="~/R/GSM3733316_E59_distal_femur_peaks_hg19.bed.gz")
#if you unzip 
> 
> export.wig(object=bed_loaded, con="~/R/bed2wig.wig") Error in .local(object, con, format, ...) :    The score must be numeric, without any NA's

I just start to use R, could someone help me? Thanks in advance!!

[Pierre Lindenbaum]

Converstion of BED with scores into bigWig

Answer 1

[ATpoint]

This is not possible. Bigwigs are based on BED files with scores which you do not have. You only have peak coordinates. If you want to see a browser track with actual peaks (so the pileup of the reads), then you have to start from the bam files, see for example bamCoverage from deeptools.

[kuangliang128]

I see, thanks a lot!！