I have RNASeq aligned bam files from tophat for human samples and I need to find out the percent reads mapped to rRNA( apart from mapped reads to exonic, intronic and intergenic). Can anyone suggest on how to get these alignment statistics for the rRNAs ( based on feature tag rRNA in 2nd column of the gtf file)? I could find lot of posts about the exonic, intronic and intergenic % mapped but not rRNA. I have the gtf file with the annotations for all regions.
Thanks a lot!