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?
Question: How can I count reads mapped to the ribosomal genes.
2.5 years ago by
biplab • 100
University of California, Davis
biplab • 100 wrote:
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