0
0
Entering edit mode
kavator ▴ 20
@kavator-22955
Last seen 10 days 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 • 61 views
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.