I want to know how many reads are coming from rRNA in my data. My librairies are done with illumina TruSeq (Stranded) and RiboZero. So here my idea.
In UCSC Tables :
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
Now I've a gtf file with the rRNA and the tRNA
After that, I use htseq-count to extract the number of reads per rRNA and tRNA gene.
Is that ok ?