Hi.
I've been searching everywhere for this, and I can't find a clear answer.
I am mapping RNAseq reads to the human genome using Bowtie2. I am only looking for reads that align ONLY ONCE to the genome. By default Bowtie2 reports all the reads that are aligned. Is there an option so I only have unique mapping reads in my sam file?
Any help would be appreciated. Thanks!
I've been searching everywhere for this, and I can't find a clear answer.
I am mapping RNAseq reads to the human genome using Bowtie2. I am only looking for reads that align ONLY ONCE to the genome. By default Bowtie2 reports all the reads that are aligned. Is there an option so I only have unique mapping reads in my sam file?
Any help would be appreciated. Thanks!
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