can you give more detail about the kind of figure you want to make? 

I am very enthusiast about nice figure :)

Lovorka, what would you like to represent in this figure (abundance)?

For example, the R package CummeRbund has the possibility to represent your transcripts (RNAseq reads) mapped to your reference genome (together with there abundances).

Looking forwards the discussion.

Cheers.

You can also use IGV (https://www.broadinstitute.org/igv/) and zoom in to the region of interest.

Thanks for your fast replies.

Yes I am a looking at the abundance of lncRNAs using RNA seq after depleting them with different methods. Does CummeRbund works for lima voom or only for Cufflinks?

you can use circos for whole genome and zoom in your specific locus .  

sashimi plot - eg from IGV