Need a sugestion about Wiggle Plots Graph

[Romualdo]

Hi everybody, I have a own mitochondrial genome (a fasta and gff3), and i have a transcripts.gtf (output from Cufflinks), and I need make a pretty and simple Wiggle Plots Graph, tried UCSC but I cant find a way to use my genome on it, tried IGV without sucess too (I cant find option to make graphs), and the SeqMonk without sucess too.

I need a suggestion of a application or way to do it simple.

[id0]

The GTF file will only have exon boundaries. You need to generate the Wig or BigWig or TDF files from the BAM files. You can then input those into IGV.