I downloaded a GRO-Seq dataset from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38140 and got a bedGraph file that's 4.2gb large.
I wanted to generate heatmaps of sense and antisense strands using deeptools, which requires a bigWig file format. I figured it'd be pretty simple using a bdg2bw script found here but I received this error:
$ /Users/Carlos/Dropbox/bdg2bw Gro-Seq.bdg /Users/Carlos/Desktop/Projects/GenomicDataPublication_Project/Gencode/hg19.chrom.sizes
Overlapping regions in bedGraph line 44 of Gro-Seq.bdg.clip
Not quite sure what to do to fix this. I know it's pretty simple in concept, just remove overlapping regions. But I'm not sure how exactly to go about doing that or if it would bias the results or something just as terrible, of the heatmap if I did.