Question: Is there a tool for calculating the number of uniquely mapped reads, ambigiously mapped reads, and unmapped reads from sam/bam?

gravatar for O.rka

3 hours ago by

I found a tool called MMQuant but this is suppose to be drop in replacement (though, it's not) for featureCounts. I'm trying to calculate the number of uniquely mapped reads, the number of ambigiously mapped reads, and the number of unmapped reads.

Is there a tool that can calculate these basic measures for sam/bam files?


modified 3 hours ago

3 hours ago


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