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Old 07-24-2017, 11:22 AM   #103
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Originally Posted by Brian Bushnell View Post
You have 4.5 billion reads, and expect to detect contamination from 11% of the data (0.5B/4B)
Yeah, sounds reasonable. But I guess there is still the question of whether the index hop derives from a characteristic of the donor library, the recipient library or both? Illumina is saying that the index donor library definitely plays a role when said library includes unincorporated adapters and/or adapter dimers.

This seems like a really high rate of recombination, no? Do you detect an increase in chimeric inserts? Depending on the mechanism of recombination you stipulate, there might be recombination events at any stretch of similar sequence, not just in the adapters.

Originally Posted by Brian Bushnell View Post
at a 90%-100% rate (alignment sensitivity) by observing 89% of data volume (4B/4.5B). So you should expect to detect .11*.89*(.9 to 1) = 8.8% to 9.8% of the total contamination. So, 2000 PPM observed would suggest 20400 PPM to 22700 PPM of actual cross-contamination, with a sufficiently high degree of multiplexing.

Bear in mind, though, that mouse contamination can come from other sources, and different index pairs have different rates of cross-contamination.
These were run as single indexes. But there may be different rates, yes.

I checked the HiSeq run for these environmental samples and we detected 0/1000 reads mouse hits for all 21 of the data sets.

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