Question: How can I count reads mapped to the ribosomal genes.
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2.5 years ago by
University of California, Davis
biplab100 wrote:

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?

rna-seq alignment next-gen • 821 views
ADD COMMENTlink written 2.5 years ago by biplab100

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.

ADD REPLYlink written 2.5 years ago by genomax85k

Thank you so much for help.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by biplab100
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