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Old 12-17-2016, 05:21 PM   #403
Brian Bushnell
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Location: Walnut Creek, CA

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It would be useful to know what the ambiguous reads are hitting. It's likely that it's something with many copies, such as ribosomal elements. Ribo "contamination" is common in libraries even when some kind of ribo-depletion is used. You can catch the ambiguous reads with a second mapping pass using "ambig=toss outu=unmapped.fq" if you start with just the mapped reads. Then, you can BLAST them, or map them again and look at an annotated version of the reference to see what they're hitting. But it's likely ribosomal.
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