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Old 12-16-2016, 07:44 PM   #401
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,696

Normally... I see ambig rates of 3% or lower in diploids like human, and 0.1% or lower in haploid bacteria. I have little experience in mapping RNA to plant genomes, aside from feedback from co-workers. And they mainly map to plant transcriptomes rather than genomes.

Can you describe your mapping protocol in more detail? For example, are you concatenating all genomes and mapping to all simultaneously, or are you experiencing a high claimed ambig rate when mapping to a single reference alone?
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