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Old 11-27-2012, 04:14 AM   #5
knostrov
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Location: Boston

Join Date: Oct 2012
Posts: 7
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Thank you for the quick replies. Actually I have by now realized that almost all of these contaminating sequences are reads that consist of nothing but adapter sequence, e.g. 50bp of read2-primersite--tag--adapter. I imagine those must be two linked adapters with no insert in between. One would think such constructs would be eliminated by size selection? Also their abundance varies per sample. They make up between 2-25% of all reads, depending on the sample.

So the specifics of this sequencing experiment are (I did not do the experimental part myself...)
- FFPE tissue samples, good DNA quality according to size distribution on gel
- target enrichment using the Haloplex protocol (custom probes that hybridize to the two ends of a desired region to make a circle --> ligation --> circle amplification)
- 50 bp PE run on HiSeq 2000
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