How can I count reads mapped to the ribosomal genes.

Question

[biplab]

There are two ribosomal genes(RDN37-1, RDN37-2) in my genomic sequence file, both have same sequence. Therefore when I did the alignment by bowtie2, reads that mapped to ribosomal genes mapped both regions thus low mapping quality for those reads. After mapping when I used htseq-count in order to count read mapped to features RDN37-1 and RDN37-2 give 0 count because low quality mapping. In this case, what will be best way to count reads for RDN37-1?

[GenoMax]

I think the option for htseq-count to count multi-mapped reads is --nonunique all. Equivalent command for featureCounts is -M. Both programs will not count multi-mappers by default.

[biplab]

Thank you so much for help.