convert local downloaded bigwig files to .bed files
0
0
Entering edit mode
kavator ▴ 30
@kavator-22955
Last seen 15 months ago
Singapore

Hi im trying out the new BRGenomics package with some hope to convert a publicly available chipseq (GSE106666) BigWig files to .bed files for further analyses; I saw the tutorial for BRgenomics that the + and - strand has to be specified for import_bigWig() function; but to the best of my understanding; the locally downloaded BigWig files from GSE106666 is a merged file of both + and - strands(?).

I was wondering if there's a way to go about this to import those bigwig files into Rstudio? and also to subsequently convert it into .bed files

thank you!

BRgen BRGenomics • 1.3k views
ADD COMMENT
0
Entering edit mode

What is the problem? import_bigWig does the import of bigwig into R. Yes, bigwig is an unstranded format. For stranded information you would need to create bigwigs per strand based on the alignment (BAM) files. You cannot infer strand from just a bigwig.

ADD REPLY

Login before adding your answer.

Traffic: 940 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6