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question about ILLUMINACLIP 2:30:10 #52

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ghost opened this issue Jul 18, 2023 · 0 comments
Open

question about ILLUMINACLIP 2:30:10 #52

ghost opened this issue Jul 18, 2023 · 0 comments

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@ghost
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ghost commented Jul 18, 2023

Hello,

I have difficulties to understand the meaning of "2:30:10" for adaptor removal command.
The manual of Trimmomatic describes:

ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold> 

seedMismatches: specifies the maximum mismatch count which will still allow a full match to be performed

palindromeClipThreshold: specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment.

simpleClipThreshold: specifies how accurate the match between any adapter etc. sequence must be against a read

What exactly is the "ClipThreshold" and how are the values (30 and 10) calculated?

Many thanks in advance,

silviac

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