Today maybe very specific hint, but some of you may find it useful. I was looking for a way of incorporating the data from GEO in jBrowse. First, I’ve generated BED file out of results in proprietary format, then I have converted this to bedGraph and bigWig following the hint from BioStars.
transcript2genomic.py is available through github.

# convert GEO to BED
zcat GSE53693_allinfo_final_ORFs.txt.gz | cut -f3,4,9 | transcript2genomic.py ../../ref/DANRE.gtf > GSE53693.bed
 
# BED 2 BedGraph
sort -k1,1 -k2,2n GSE53693.bed | bedtools merge -scores max | awk '{printf "%s\t%d\t%d\t%2.3f\n" , $1,$2,$3,$4}' > GSE53693.bg
# using bedtools2
#sort -k1,1 -k2,2n GSE53693.bed | bedtools merge -c 5 -o max | awk '{printf "%s\t%d\t%d\t%2.3f\n" , $1,$2,$3,$4}' > GSE53693.bg
 
# bedGraph 2 BigWig
bedGraphToBigWig GSE53693.bg ../../ref/DANRE.fa.fai GSE53693.bw