mm39 rRNA bed file

[payal banerjee]

Hello,

Please direct how to download rRNA bed file for mm39 from UCSC genome browser. They don't have specific rRNA track. 

I downloaded the mm39 gtf file from Gencode. Then extracted just the rRNA.I used BEDOPS gtftobed to covert to bed file. The output is not compatible with Rseqc. 

I also tried with just three columns  - chromosome, start and end position. Nothing works. Please provide guidance how create rseqc compatible BED file. 

Thanks,

Payal