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Old 06-16-2015, 01:45 AM   #18
Brian Bushnell
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Location: Walnut Creek, CA

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Originally Posted by pmiguel View Post
Actually that is pretty much what all 600 cycle runs seem to do. Oddly 500-550bp amplicons seems to PANDA merge just fine, so I tended to assume that the instrument was just losing its confidence. But since the phiX error rate also tends to sky rocket at this point, I am not sure what to think.

This won't work for the amplicon reads, but for the PhiX reads, you can plot the error rates like this: nodisk ref=phix.fa in=reads.fq mhist=mhist.txt qhist=qhist.txt ehist=ehist.txt

As long as you have at least a few percent of PhiX, it should be somewhat reflective of the error rates by position of all reads. You can use all reads for this, or just the PhiX reads; the results will be similar, since non-PhiX reads won't map to PhiX. However, it will be slightly more accurate using all reads, since that will include reads that are so low quality that Illumina's software does not recognize them as PhiX.

Last edited by Brian Bushnell; 06-16-2015 at 01:49 AM.
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