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Old 10-20-2016, 09:12 PM   #3
finswimmer
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Location: Europe

Join Date: Oct 2016
Posts: 60
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Hello husamia,

we always check the fragment size of our library with a Bioanalyzer. There the library show a normal distribution of the fragment sizes. Also cluster density, cluster passing filter, Q Values, percentage of total aligned reads, the distribution of samples within the library looks fine.

There are only two values that are abnormal:
- the mentioned high percentage of off-target reads
- the concentration of the library after preperation. It's up to 3-4 times higher than normally. That's why we guess it has something to do with the capture or washing step. Either the hybridization probes captured to much or within the washing step to much unspecific region stay in the sample.

So maybe it's possible to check the concentration with Qubit after washing and if it's to high (but what is "to high"?) we can repeat one more wash?

fin swimmer

Last edited by finswimmer; 10-20-2016 at 09:16 PM.
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