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If I give a command for AVGQUAL:20 without sliding window will it set any default values for the slidingwindow?

Vaisakh Viswanath
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  • I took a look at the Java source code and didn't see any obvious default values, but you're probably going to have to ask the authors to get a confirmed answer. – nbryans Jun 15 '17 at 14:21
  • Thank you @nbryans ,I also went through the paper and there also they dont mention any default values – Vaisakh Viswanath Jun 15 '17 at 15:16

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If you check the trimmmomatic website http://www.usadellab.org/cms/?page=trimmomatic , you will find the manual there.

In the manual it says for AVGQUAL: AVGQUAL: Drop the read if the average quality is below the specified level

Therefore no window is needed, as this step sums up all qualities, divides by length and checks whether the threshold is reached or not, and then drops or retains the read.

mjoppich
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