Hi every body,
I am trying to count the number of reads aligned to rRNA. The genome that I am working on it (Salmonella) has seven copies of rRNA genes. So it is normal that reads that relate to rRNA are aligned to multiple loci on the genome. I just want to know the percentage of reads that are aligned to rRNA so I have to count each of these reads only for one time whereas tools like HTSeq that are regularly used for counting reads are not able to do that. For example when I tell HTSeq to count non uniquely aligned reads, It counts them for multiple times and the final total number of reads are more than the total reads that I have in my sample.
Does any one know any appropriate tool for doing this? Thanks a lot