Question: How to convert BED file of ATAC seq to Bigwig file
gravatar for kuangliang128
4 weeks ago by
kuangliang1280 wrote:

enter image description here

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!!

atat-seq • 119 views
ADD COMMENTlink modified 4 weeks ago by GenoMax96k • written 4 weeks ago by kuangliang1280

Converstion of BED with scores into bigWig

ADD REPLYlink written 4 weeks ago by Pierre Lindenbaum134k
gravatar for ATpoint
4 weeks ago by
ATpoint46k wrote:

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.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by ATpoint46k

I see, thanks a lot!!

ADD REPLYlink written 29 days ago by kuangliang1280
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1060 users visited in the last hour