For all the the folks who are doing RNA-Seq analysis and looking for a comprehensive annotation (esp. for the human genome), I found a decent table in the Supplementary materials of the paper by Cabili et al. (Integrative Annotation of Human Large Intergenic Non-Coding RNAs Reveals Global Properties and Specific Subclasses, Genes Dev., Sept 2, 2011) pubmed. These annotations prove to be very useful during the filtering of transcripts after the transcriptome assembly. rRNA and tRNA gtf file can be supplied to Cufflinks (using -M option) during the assembly process in order to exclude reads mapping to these RNAs. Exclusion of such reads can improve abundance estimates of other more useful (protein coding, lincRNAs etc) transcripts.
I am pasting the table below:
I am pasting the table below:
