How to get tRNA/rRNA/mitochondrial gene GTF file

Cufflinks/Tophat ask for a GTF file to mask the abundant transcripts (e.g. tRNA/rRNA/chrM). Here is the step to get such a file:

Go to UCSC Table browser:

For tRNA/rRNA:

    * Select "All Tables" from the group drop-down list
    * Select the "rmsk" table from the table drop-down list
    * Choose "GTF" as the output format
    * Type a filename (e.g. "rRNA.tRNA.gtf") in "output file" so your browser downloads the
result
    * Click "create" next to filter
    * Next to "repClass," type rRNA
    * Next to free-form query, select "OR" and type repClass = "tRNA"
    * Click submit on that page, then get output on the main page

For chrM genes:

    * Select "All Tables" from the group drop-down list
    * Select the "knownGene" table from the table drop-down list
    * Choose "GTF" as the output format
    * Type a filename (e.g. "chrM.gtf") in "output file" so your browser downloads the result
    * Click "create" next to filter
    * Next to "chrom," type chrM
    * Click submit on that page, then get output on the main page

cat the two files from above steps. That's it. 
P.S.  I just noticed that for galgal3 (chicken), UCSC does not have rRNA/tRNA in the repeat database.