I would like to run CollectRNASeqMetrics to calculate amount of rRNA in my RNA seq aligned data. Are they already available REF_FLAT and RIBOSOMAL_INTERVALS files that one can use? If not how do you make these files? Thanks!
Just so you know, this is beyond the scope of what we can support. Having said that... I have read that the following website: http://central.biomart.org/martwizard/#!/Search_by_database_name?mart=Ensembl+82+Genes+(WTSI%2C+UK)&step=1&datasets=hsapiens_gene_ensembl enables the user to generate these interval files. In addition, I have also read that http://www.arb-silva.de/ is a good resource for these files. Finally, there are several discussions regarding this topic including the following which might be helpful, https://www.biostars.org/p/67079/
Hope this helps.