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?
Hello,
I have difficulties to understand the meaning of "2:30:10" for adaptor removal command. The manual of Trimmomatic describes:
What exactly is the "ClipThreshold" and how are the values (30 and 10) calculated?
Many thanks in advance,
silviac