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Old 12-08-2012, 07:35 AM   #1
apredeus
Senior Member
 
Location: Bioinformatics Institute, SPb

Join Date: Jul 2012
Posts: 151
Default High percentage of N calls in the library

hello all,

I've discovered an peculiar feature in the libraries that I'm working with using FastQC

The percentage of "N" calls is dramatically higher for base #11. It's at ~ 10% level (as opposed to << 1 % for all other positions). This persists across several libraries and it's always the base #11. The reads are 42 nt long.

Does this mean there was some problem with the instrument? Can't imagine it would be something in the library construction...

Otherwise base call Phred scores are in good to excellent range. The library is also very repetitive.
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