Tuesday, February 14, 2012

get rRNA.gtf file from UCSC Table Browser

You can get this pretty easily from the UCSC table browser (http://genome.ucsc.edu/cgi-bin/hgTables).

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 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


  1. Anonymous12:36 PM

    thank you!

  2. Replies
    1. tRNA loci reads encompass a large fraction of total RNA-seq reads in many experiments. Like rRNA fragments, relative tRNA fragment abundance sequenced across similar experiments is highly variable. Excluding these highly variable, high abundance reads from FPKM or RPKM calculations generally lead to more accurate/repeatable quantification.

  3. UCSC is a very usedul tools, but I still not clear about the use of it. Thanks for your tips!