Hi Everyone 

I converted the gtf file I got from stringtie to bed. 
The bed still contains the stringtie gene and transcripts code (same thing if I used cufflinks instead) , is there a way to post-process this bed file to have real gene names and transcripts not stringtie nor cufflinks ids:

    chrY	23451597	23451912	STRG.80985.1	0	.	23451597	23451912	0	1	315,	0,
    chrY	23460655	23460996	STRG.80986.1	0	.	23460655	23460996	0	1	341,	0,
    chrY	23464508	23464868	STRG.80987.1	0	.	23464508	23464868	0	1	360,	0,
   

Thanks
You could use BEDOPS `bedmap` to annotate regions with genes (or their names):

    $ bedmap --echo --echo-map-id regions.bed genes.bed > answer.bed

If you edit your question to note the genome you're working with, I can suggest where to get annotations to build the `genes.bed` file.