I am using Trimmomatic to improve the quality of my RNA-seq data. I am using the following tools:
ILLUMINACLIP:<fastawithadaptersetc>:<seed mismatches="">:<palindrome clip="" threshold="">:<simple clip="" threshold=""> fastaWithAdaptersEtc: specifies the path to a fasta file containing all the adapters, PCR sequences etc. The naming of the various sequences within this file determines how they are used. See below. 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.
LEADING:<quality> quality: Specifies the minimum quality required to keep a base.
TRAILING:<quality> quality: Specifies the minimum quality required to keep a base.
I am not sure what to input for the above values. For Illuminaclip I ran 2 (seedMismatches), 30 (palindromeClipThreshold), and 10 (simpleClipThreshold). I ran 30 (phred score?) for leading and trailing quality.
Are these numbers correct?
Also, what adapter file should I use?