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.